3SW6 | pdb_00003sw6

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase covalently modified by 5-fluoro-6-azido-UMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DV7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	Trisodium Citrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.118	α = 90
b = 103.37	β = 90
c = 73.92	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 315		2007-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90020	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	50	99.6	0.049	13.4	5.6	35880	34615

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	1.5	1.53	99.2		0.374	3.57	5	1770

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	1DV7	1.5	50	34062	1792	99.59	0.16236	0.16097	0.16	0.18909	0.19	RANDOM	15.78

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]
0.32			-0.54		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.745
r_dihedral_angle_4_deg	19.519
r_dihedral_angle_3_deg	12.902
r_dihedral_angle_1_deg	5.419
r_scangle_it	3.993
r_scbond_it	2.362
r_mcangle_it	1.505
r_angle_refined_deg	1.46
r_mcbond_it	0.833
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.745
r_dihedral_angle_4_deg	19.519
r_dihedral_angle_3_deg	12.902
r_dihedral_angle_1_deg	5.419
r_scangle_it	3.993
r_scbond_it	2.362
r_mcangle_it	1.505
r_angle_refined_deg	1.46
r_mcbond_it	0.833
r_chiral_restr	0.093
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1622
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	22

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.