6ZSP | pdb_00006zsp

Human serine racemase bound to ATP and malonate.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L6B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	25% PEG 3350 230 mM sodium malonate 15 mM magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.943	α = 90
b = 81.191	β = 90
c = 134.468	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS EIGER2 XE 16M		2018-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.978	Diamond	I03

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	1.6	50.1	97.5	0.069	0.079	0.999	9.2	4		76688

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	1.6	1.63	81		0.577	0.705	0.512	1.3	2.5

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	THROUGHOUT	3L6B	1.6	42.651	75542	3722	96.017	0.194	0.1923	0.19	0.226	0.23	21.499

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]
-0.556			0.546		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.033
r_dihedral_angle_4_deg	20.212
r_dihedral_angle_3_deg	13.416
r_dihedral_angle_1_deg	6.113
r_lrange_it	5.21
r_scangle_it	1.927
r_mcangle_it	1.689
r_angle_refined_deg	1.326
r_scbond_it	1.168
r_mcbond_it	0.992
r_nbtor_refined	0.306
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.163
r_symmetry_nbd_refined	0.152
r_chiral_restr	0.095
r_metal_ion_refined	0.008
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4800
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	121

Software

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