2O4C | pdb_00002o4c

Crystal Structure of D-Erythronate-4-phosphate Dehydrogenase Complexed with NAD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	297	0.7M ammonium dihydrogen phosphate, 0.4M ammonium tartrate, 0.1M sodium citrate (pH 5.6), 10mM cupric chloride, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.76	67.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.914	α = 90
b = 101.63	β = 90
c = 142.994	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 210	mirrors	2004-06-25	M	MAD
2	1	x-ray	100	CCD	ADSC QUANTUM 210	mirrors	2004-06-25	M	SINGLE WAVELENGTH
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.97930, 0.97946, 0.95000	Photon Factory	AR-NW12A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.00000	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
1,2	2.2	30	99.9	0.049	14.6			63477

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.2	2.28	100		0.442			6245

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	MAD	THROUGHOUT	2.3	19.77	55468	5563	99.83	0.229	0.225	0.22	0.259	0.26	RANDOM	44.484

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.975
r_dihedral_angle_4_deg	18.437
r_dihedral_angle_3_deg	15.72
r_dihedral_angle_1_deg	5.229
r_scangle_it	2.073
r_scbond_it	1.283
r_angle_refined_deg	1.173
r_mcangle_it	0.99
r_mcbond_it	0.589
r_nbtor_refined	0.297

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5772
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	109

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

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.