X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details 0.1M HEPES PH 7.5, 12%PEG, 0.2M MGCL2. PROTEIN WAS OXIDIZED WITH A 1:1.25 MOLAR RATIO OF H2O2 - PROTEIN PRIOR TO CRYSTALLIZATION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.22 α = 90
b = 88.22 β = 90
c = 103.79 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2002-07-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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
1.75 50 99.5 0.039 -- -- 7.07 -- 43606 -- -- --
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)
1.8 1.84 99.3 0.355 -- 26.26 -- --

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 1.8 76.7 -- -- -- 41389 2217 99.5 -- 0.204 0.203 0.227 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 1.8 1.85 -- 155 3020 0.254 0.329 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.7
Anisotropic B[1][1] 0.69
Anisotropic B[1][2] 0.34
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.69
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.03
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.211
r_gen_planes_refined 0.008
r_chiral_restr 0.14
r_dihedral_angle_1_deg 6.098
r_angle_refined_deg 1.836
r_bond_refined_d 0.02
r_xyhbond_nbd_refined 0.149
r_symmetry_vdw_refined 0.176
r_symmetry_hbond_refined 0.195
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2289
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 181

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK 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