3Q11 | pdb_00003q11

Crystals Structure of Aspartate beta-Semialdehyde Dehydrogenase from Streptococcus pneumoniae with NADP and aspartyl beta-difluorophosphonate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	12 % PEG 3350, 0.1 M ammonium acetate, 0.05 M Na-citrate buffer, 10mM DTT, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.014	α = 90
b = 98.702	β = 100.79
c = 64.528	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU RAXIS IV	confocal mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	37.8	89	0.067	6.8	1.98		68322			21.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	89.1		1.6		3647

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.8	37.8	57723	3095	88.95	0.20502	0.20306	0.21	0.24177	0.25	RANDOM	30.035

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]
-0.15		-0.72	1.54		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.126
r_dihedral_angle_4_deg	15.519
r_dihedral_angle_3_deg	12.273
r_dihedral_angle_1_deg	5.668
r_scangle_it	1.575
r_angle_refined_deg	1.106
r_scbond_it	0.947
r_mcangle_it	0.557
r_mcbond_it	0.288
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.126
r_dihedral_angle_4_deg	15.519
r_dihedral_angle_3_deg	12.273
r_dihedral_angle_1_deg	5.668
r_scangle_it	1.575
r_angle_refined_deg	1.106
r_scbond_it	0.947
r_mcangle_it	0.557
r_mcbond_it	0.288
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5456
Nucleic Acid Atoms
Solvent Atoms	609
Heterogen Atoms	147

Software

Software
Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

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.