2GCI | pdb_00002gci

The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an asparte/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X74	PDB ENTRY 1X74

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	1.52M Ammonium phosphate, 10mM Barium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.7	α = 90
b = 79.81	β = 89.93
c = 118.06	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	Bent mirror	2005-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.00	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	35	97	0.063	0.063	15	4.8		214258			26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.8	94		0.274		61537

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1X74	1.6	19.83	203330	203330	10825	96.99	0.21186	0.21015	0.21	0.24	0.24413	0.25	RANDOM	28.417

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.773
r_dihedral_angle_4_deg	16.348
r_dihedral_angle_3_deg	14.776
r_dihedral_angle_1_deg	5.764
r_scangle_it	3.062
r_scbond_it	2.159
r_angle_refined_deg	1.557
r_mcangle_it	1.408
r_mcbond_it	0.977
r_symmetry_vdw_refined	0.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.773
r_dihedral_angle_4_deg	16.348
r_dihedral_angle_3_deg	14.776
r_dihedral_angle_1_deg	5.764
r_scangle_it	3.062
r_scbond_it	2.159
r_angle_refined_deg	1.557
r_mcangle_it	1.408
r_mcbond_it	0.977
r_symmetry_vdw_refined	0.365
r_nbtor_refined	0.312
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.186
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10716
Nucleic Acid Atoms
Solvent Atoms	1208
Heterogen Atoms	273

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.