5GZ6

Structure of D-amino acid dehydrogenase in complex with NADPH and 2-keto-6-aminocapronic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GZ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.838	α = 90
b = 94.773	β = 90
c = 138.791	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	CCD	ADSC QUANTUM 270	silicon single crystal	2015-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.74	50	99.8	0.116	9.2	7		74999

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	1.74	1.77	100		1.617	0.411		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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5GZ1	1.74	50	71112	3780	99.64	0.2097	0.2075	0.2502	RANDOM	35.261

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]
-0.07			0.8		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.377
r_dihedral_angle_4_deg	16.775
r_dihedral_angle_3_deg	14.152
r_dihedral_angle_1_deg	6.784
r_mcangle_it	3.892
r_mcbond_it	2.578
r_mcbond_other	2.578
r_angle_refined_deg	2.357
r_angle_other_deg	1.215
r_chiral_restr	0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.377
r_dihedral_angle_4_deg	16.775
r_dihedral_angle_3_deg	14.152
r_dihedral_angle_1_deg	6.784
r_mcangle_it	3.892
r_mcbond_it	2.578
r_mcbond_other	2.578
r_angle_refined_deg	2.357
r_angle_other_deg	1.215
r_chiral_restr	0.156
r_bond_refined_d	0.028
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4920
Nucleic Acid Atoms
Solvent Atoms	397
Heterogen Atoms	72

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.