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_symmetry_hbond_refined 0.223
r_scbond_it 2.695
r_bond_refined_d 0.015
r_chiral_restr 0.108
r_nbd_refined 0.197
r_xyhbond_nbd_refined 0.148
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 5.605
r_mcbond_it 0.898
r_scangle_it 4.623
r_mcangle_it 1.634
r_symmetry_vdw_refined 0.234
r_angle_refined_deg 1.412
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

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
AMoRE phasing
REFMAC refinement version: 5.1.24
CCP4 data scaling version: (SCALA)