X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 295.0
Details 0.1M Tris-sodium citrate buffer, 0.2M ammonium acetate, 33% polyethylene glycol 4k, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.13 α = 90
b = 101.77 β = 102.6
c = 46.32 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M mirrors 2012-11-14
Diffraction Radiation
Monochromator Protocol
channel cut cryogenically cooled monochromator crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9791 SOLEIL PROXIMA 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
1.66 38.12 99.5 0.04 -- -- 3.7 44718 44718 0.0 -3.0 23.2
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)
1.66 1.76 98.1 0.189 -- 6.9 3.5 7126

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 1.66 38.12 -- -- 44718 42482 2236 99.54 0.178 0.17661 0.17487 0.20935 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 1.66 1.703 -- 158 3011 0.27 0.3 -- 96.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.328
Anisotropic B[1][1] -0.95
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.41
Anisotropic B[2][2] -1.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.75
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.842
r_chiral_restr 0.17
r_dihedral_angle_3_deg 12.135
r_gen_planes_refined 0.013
r_dihedral_angle_2_deg 33.099
r_bond_refined_d 0.024
r_angle_refined_deg 2.342
r_dihedral_angle_4_deg 21.742
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2727
Nucleic Acid Atoms 68
Heterogen Atoms 49
Solvent Atoms 296

Software

Software
Software Name Purpose
MX data collection version: Cube
PHASER phasing
REFMAC refinement version: 5.7.0032
XDS data reduction
XSCALE data scaling