4WBT

Crystal structure of histidinol-phosphate aminotransferase from Sinorhizobium meliloti in complex with pyridoxal-5'-phosphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-I condition #94 (0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.055	α = 90
b = 64.322	β = 93.24
c = 137.048	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	CCD	MARMOSAIC 225 mm CCD	Beryllium Lenses	2014-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	99.9	0.08	0.085	0.053	9	4.6		150339		-3	15.2

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	1.6	1.63	98.6		0.574	0.625	0.387	0.679	2.38	4.2	13785

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	SAD	THROUGHOUT	1.6	50	142544	7537	99.88	0.1469	0.1461	0.1634	RANDOM	21.303

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]
0.24		-0.21	0.57		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.381
r_dihedral_angle_4_deg	21.246
r_dihedral_angle_3_deg	12.42
r_dihedral_angle_1_deg	5.845
r_angle_refined_deg	1.461
r_mcangle_it	1.276
r_angle_other_deg	1.225
r_mcbond_it	0.769
r_mcbond_other	0.768
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.381
r_dihedral_angle_4_deg	21.246
r_dihedral_angle_3_deg	12.42
r_dihedral_angle_1_deg	5.845
r_angle_refined_deg	1.461
r_mcangle_it	1.276
r_angle_other_deg	1.225
r_mcbond_it	0.769
r_mcbond_other	0.768
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8214
Nucleic Acid Atoms
Solvent Atoms	1024
Heterogen Atoms	96

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-3000	data collection
HKL-3000	phasing
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.