7NBD | pdb_00007nbd

Crystal structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen.

X-RAY DIFFRACTION

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Starting Model(s)

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

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
2.1	41.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.012	α = 90
b = 154.846	β = 98.043
c = 85.451	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		2018-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91578	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.86	84.61	94	0.073	0.1	0.998	8.9	3.5		96340			37.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.97	82		0.912	0.47	1.1	3.5

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	6ZUJ	1.865	84.6	96297	4830	93.91	0.178	0.1762	0.18	0.2074	0.21	37.903

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]
-0.245		0.231	0.293		-0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.249
r_dihedral_angle_4_deg	22.343
r_dihedral_angle_3_deg	15.291
r_lrange_it	11.187
r_dihedral_angle_1_deg	6.162
r_scangle_it	4.707
r_mcangle_it	3.407
r_scbond_it	3.189
r_mcbond_it	2.279
r_angle_refined_deg	1.669
r_symmetry_xyhbond_nbd_refined	0.326
r_nbtor_refined	0.314
r_symmetry_nbd_refined	0.264
r_nbd_refined	0.253
r_xyhbond_nbd_refined	0.239
r_metal_ion_refined	0.171
r_symmetry_metal_ion_refined	0.117
r_chiral_restr	0.114
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9472
Nucleic Acid Atoms
Solvent Atoms	1053
Heterogen Atoms	179

Software

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