X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 5mM MES, 200mM NaCl, 100mM MES, 26% polyethylene glycol 400 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.89 α = 90
b = 67.89 β = 90
c = 129.9 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS VII -- 2013-09-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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
2 50 95.9 -- 0.091 -- -- -- 38003 -- -- --
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)
2.0 2.07 93.0 -- 0.357 3.0 -- --

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 2.0 20.0 -- -- -- 35981 1941 95.75 -- 0.24177 0.23901 0.295 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 1.999 2.051 -- 139 2472 0.328 0.319 -- 90.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.307
Anisotropic B[1][1] 6.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.73
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 8.187
r_chiral_restr 0.288
r_gen_planes_refined 0.01
r_scangle_it 6.43
r_scbond_it 5.06
r_dihedral_angle_3_deg 20.796
r_mcangle_it 2.76
r_bond_refined_d 0.009
r_angle_refined_deg 4.241
r_dihedral_angle_4_deg 15.951
r_dihedral_angle_2_deg 38.913
r_mcbond_it 1.902
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2392
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 174

Software

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