8PNX

Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens in PMP form

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q1R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	0.1 M Hepes pH 7.5, 4 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.437	α = 90
b = 105.437	β = 90
c = 51.144	γ = 120

Symmetry
Space Group	P 31 2 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	RIGAKU HyPix-6000HE		2022-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54184

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	20.55	99.2	0.111	0.114	0.028	0.999	23.2	15.9		30325

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	1.84		95.9	0.462	0.482	0.133	0.836		12.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	20.55	28882	1431	99.1	0.17795	0.17628	0.21079	RANDOM	10.965

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]
2.32			2.32		-4.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.644
r_dihedral_angle_3_deg	15.966
r_dihedral_angle_4_deg	15.68
r_dihedral_angle_1_deg	6.531
r_long_range_B_refined	3.675
r_long_range_B_other	3.546
r_scangle_other	2.031
r_mcangle_it	1.781
r_mcangle_other	1.78
r_angle_refined_deg	1.75
r_angle_other_deg	1.425
r_scbond_it	1.288
r_scbond_other	1.287
r_mcbond_it	1.086
r_mcbond_other	1.084
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2020
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CrysalisPro	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction