X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 0.1 M Hepes, pH 7.5, 30 % w/v PEG 400, 0.2 M MgCl2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.52 α = 90
b = 126.52 β = 90
c = 103.21 γ = 120
Symmetry
Space Group P 6 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2014-07-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.127092 SSRL BL7-1

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
1.56 38.44 91.1 0.06 -- -- 11.1 -- 62486 -- -- --
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)
1.56 1.59 79.3 0.522 -- 2.7 5.9 2642

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 1.56 38.44 -- -- -- 59427 3059 90.26 -- 0.10375 0.10219 0.13422 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 1.562 1.602 -- 207 3979 0.162 0.188 -- 83.37
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.422
Anisotropic B[1][1] 0.46
Anisotropic B[1][2] 0.23
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.48
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_refined 4.283
r_chiral_restr 0.118
r_scbond_other 3.725
r_angle_other_deg 1.22
r_sphericity_bonded 10.736
r_bond_refined_d 0.017
r_gen_planes_other 0.004
r_long_range_B_other 3.809
r_sphericity_free 31.261
r_mcangle_other 2.704
r_mcangle_it 2.664
r_dihedral_angle_3_deg 14.045
r_dihedral_angle_1_deg 6.139
r_mcbond_other 2.232
r_angle_refined_deg 1.84
r_dihedral_angle_4_deg 21.016
r_gen_planes_refined 0.01
r_scbond_it 3.726
r_bond_other_d 0.002
r_dihedral_angle_2_deg 33.323
r_scangle_other 4.11
r_mcbond_it 2.34
r_rigid_bond_restr 7.176
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2473
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 390

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
XDS data reduction
Aimless data scaling
PHASER phasing