X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.2
Temperature 293.0
Details AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K. The crystals of the native enzyme (containing Mg2+ or Zn2+) have been soaked in 1 mM solution of AuCl3

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.28 α = 90
b = 92.46 β = 90
c = 138.18 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Toroidal mirror 2002-07-13
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 1.0377, 1.0404, 0.9392 ESRF ID14-4

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
1.69 46.13 88.8 0.061 0.061 -- 3.7 31884 31884 0.0 0.0 19.709
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)
1.69 1.79 53.0 0.093 0.093 7.0 1.6 2976

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
MOLECULAR REPLACEMENT 1.69 46.13 0.0 0.0 31884 31884 1673 88.8 0.17906 0.17906 0.17759 0.20698 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 1.69 1.79 2976 148 292 0.284 0.276 -- 53.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.602
Anisotropic B[1][1] 1.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.91
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.623
r_bond_refined_d 0.015
r_angle_refined_deg 1.412
r_dihedral_angle_1_deg 5.605
r_chiral_restr 0.108
r_gen_planes_refined 0.006
r_nbd_refined 0.197
r_xyhbond_nbd_refined 0.148
r_symmetry_vdw_refined 0.234
r_symmetry_hbond_refined 0.223
r_mcbond_it 0.898
r_mcangle_it 1.634
r_scbond_it 2.695
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1643
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 284

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
AMoRE model building
SCALA data reduction
MOSFLM data collection