X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 298.0
Details 0.05 M potassium phosphate, 26% Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.44 α = 90
b = 136.44 β = 90
c = 121.67 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ confocal 2003-11-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --

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
1.96 50 94.2 0.045 -- -- 3.3 41587 37497 0.0 0.0 20.0
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)
1.96 2.01 71.0 0.33 -- -- -- --

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 1.96 40.0 -- -- 39800 37497 1979 95.18 -- 0.16643 0.16339 0.22336 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 1.958 2.008 1496 77 1496 0.28 0.337 -- 52.16
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 16.937
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 2.514
r_scangle_it 4.146
r_dihedral_angle_3_deg 16.505
r_angle_refined_deg 1.906
r_dihedral_angle_1_deg 6.568
r_dihedral_angle_2_deg 35.865
r_dihedral_angle_4_deg 16.158
r_chiral_restr 0.133
r_bond_refined_d 0.021
r_scbond_it 3.082
r_gen_planes_refined 0.01
r_mcangle_it 3.528
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4658
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 336

Software

Software
Software Name Purpose
CrystalClear data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
HKL-2000 data reduction
HKL-2000 data scaling