6SLH | pdb_00006slh

Conformational flexibility within the small domain of human serine racemase.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HMK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	100 mM Bis-Tris pH 6.5, 15% PEG 3350, 250 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.2	α = 90
b = 155.74	β = 98.48
c = 85.58	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 6M		2016-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.89	40.87	99.2	0.071	10.5	3.4		98693

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.92			1.086	1.5	3.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3HMK	1.89	40.87	98652	4925	99.168	0.174	0.1723	0.17	0.2158	0.22	53.157

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]
-1.246		0.869	1.593		-0.581

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.977
r_dihedral_angle_4_deg	20.781
r_dihedral_angle_3_deg	16.436
r_lrange_it	14.358
r_dihedral_angle_1_deg	6.974
r_scangle_it	4.561
r_mcangle_it	4.165
r_scbond_it	3.059
r_mcbond_it	2.662
r_angle_refined_deg	1.859
r_nbtor_refined	0.314
r_symmetry_nbd_refined	0.285
r_metal_ion_refined	0.244
r_nbd_refined	0.24
r_symmetry_xyhbond_nbd_refined	0.179
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.127
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9302
Nucleic Acid Atoms
Solvent Atoms	532
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing