6ZUJ | pdb_00006zuj

Human serine racemase holoenzyme from 20% DMSO soak (XChem crystallographic fragment screen).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SLH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	293	100 mM MES pH 6.2 100 mM calcium chloride 5% ethylene glycol 20% PEG Smear Broad

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.062	α = 90
b = 154.998	β = 98.26
c = 85.652	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 PILATUS 6M-F		2018-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.8	84.764	97.8	0.068	0.081	0.043	0.997	9.46	3.41		111815

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	95.61		0.704	0.829	0.436	0.651	1.69	3.54

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	6SLH	1.8	84.764	111681	5508	97.639	0.181	0.1789	0.18	0.2198	0.22	34.405

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]
0.012		0.528	-0.247		0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.181
r_dihedral_angle_4_deg	21.498
r_dihedral_angle_3_deg	14.485
r_lrange_it	9.435
r_dihedral_angle_1_deg	6.449
r_scangle_it	2.579
r_mcangle_it	2.325
r_scbond_it	1.635
r_mcbond_it	1.39
r_angle_refined_deg	1.319
r_nbtor_refined	0.307
r_symmetry_nbd_refined	0.284
r_nbd_refined	0.233
r_symmetry_xyhbond_nbd_refined	0.215
r_metal_ion_refined	0.173
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.1
r_symmetry_metal_ion_refined	0.04
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9412
Nucleic Acid Atoms
Solvent Atoms	792
Heterogen Atoms	136

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing