3GW7

Crystal structure of a metal-dependent phosphohydrolase with conserved HD domain (yedJ) from Escherichia coli in complex with nickel ions. Northeast Structural Genomics Consortium Target ER63


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.0
Details Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl pH 7.5. Reservoir solution: 100mM Tris-HCl, 1M Lithium sulfate, 10mM Nickel chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.41 α = 90
b = 99.41 β = 90
c = 130.63 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Mirrors 2005-09-23
Diffraction Radiation
Monochromator Protocol
Si(111) CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.1000 NSLS X29A

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
3.3 30 97.4 0.054 0.04 -- 3.8 21299 21299 0.0 0.0 91.3
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.3 3.42 91.3 0.338 0.297 2.32 3.2 2180

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 3.3 20.0 2.0 2.0 21299 18064 1627 83.4 0.266 0.263 0.26 0.294 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.3 3.42 1101 95 1006 0.353 0.346 0.036 50.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 121.1
Anisotropic B[1][1] 10.697
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 10.697
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -21.394
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.5
c_bond_d 0.01
c_improper_angle_d 0.91
c_angle_deg 1.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.45
Luzzati Sigma A (Observed) 0.67
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.52
Luzzati Sigma A (R-Free Set) 0.74
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3398
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 0

Software

Software
Software Name Purpose
CNS refinement version: 1.2
PDB_EXTRACT data extraction version: 3.00
ADSC data collection version: Quantum
HKL-2000 data reduction
SCALEPACK data scaling
SOLVE phasing
RESOLVE phasing
REFMAC refinement