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


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
Space Group P 63


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
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline

Data Collection

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


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 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