3BS8 | pdb_00003bs8

Crystal structure of Glutamate 1-Semialdehyde Aminotransferase complexed with pyridoxamine-5'-phosphate From Bacillus subtilis

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	100mM Bicine, 30%(w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.251	α = 90
b = 55.761	β = 132.02
c = 80.504	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	MARRESEARCH		2006-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54179

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	2.3	59.761		0.07				15153

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.359					1061

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3GSB	2.3	20	14880	779	97.08	0.19547	0.19342	0.2	0.23362	0.24	RANDOM	24.336

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]
-0.38		-0.99	0.82		-1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.823
r_dihedral_angle_4_deg	18.192
r_dihedral_angle_3_deg	14.028
r_dihedral_angle_1_deg	4.724
r_scangle_it	1.452
r_angle_refined_deg	1.05
r_scbond_it	0.835
r_mcangle_it	0.561
r_mcbond_it	0.322
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.823
r_dihedral_angle_4_deg	18.192
r_dihedral_angle_3_deg	14.028
r_dihedral_angle_1_deg	4.724
r_scangle_it	1.452
r_angle_refined_deg	1.05
r_scbond_it	0.835
r_mcangle_it	0.561
r_mcbond_it	0.322
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.21
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3270
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
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 R01GM157729.