7NBF | pdb_00007nbf

Crystal structure of human serine racemase in complex with DSiP fragment Z126932614, 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
2.11	41.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.112	α = 90
b = 154.937	β = 97.957
c = 85.539	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	0.91587	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	1.599	84.716	97.6	0.059	0.082	0.997	8.9	3.3		158956			29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.599	1.63	93.4		0.658	0.889	0.383	1.1	2.7

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	1.6	84.7	158845	7962	97.468	0.173	0.1722	0.17	0.1982	0.2	28.988

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]
-0.11		0.112	0.195		-0.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.046
r_dihedral_angle_4_deg	24.948
r_dihedral_angle_3_deg	14.963
r_lrange_it	10.177
r_dihedral_angle_1_deg	6.233
r_scangle_it	4.302
r_mcangle_it	3.109
r_scbond_it	2.879
r_mcbond_it	2.002
r_angle_refined_deg	1.882
r_nbtor_refined	0.317
r_symmetry_xyhbond_nbd_refined	0.313
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.203
r_xyhbond_nbd_refined	0.189
r_metal_ion_refined	0.168
r_chiral_restr	0.127
r_symmetry_metal_ion_refined	0.056
r_bond_refined_d	0.013
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9445
Nucleic Acid Atoms
Solvent Atoms	920
Heterogen Atoms	218

Software

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