X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 7
Temperature 291.0
Details Crystallization buffer: 0.1M sodium bicine (pH 9.0), 0.2M ammonium sulfate and 2M sodium malonate (pH 7.0)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.09 α = 90
b = 41.43 β = 104.35
c = 71.65 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 PILATUS3 6M -- 2013-05-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976300 PETRA III, EMBL c/o DESY P13 (MX1)

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
0.99 41.43 96.4 -- 0.039 4.107 3.2 128596 128596 -- -- --
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)
0.99 1.04 85.0 0.262 0.262 2.9 2.8 --

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 0.99 39.72 -- 0.0 -- 115769 12806 96.24 -- 0.1268 0.1244 0.1484 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 0.988 1.014 -- 679 6435 0.183 0.196 -- 72.61
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.434
Anisotropic B[1][1] 0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.14
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 12.183
r_dihedral_angle_1_deg 7.151
r_dihedral_angle_4_deg 19.951
r_dihedral_angle_2_deg 37.498
r_sphericity_bonded 14.126
r_gen_planes_refined 0.015
r_chiral_restr 0.268
r_angle_refined_deg 2.834
r_bond_refined_d 0.025
r_sphericity_free 22.998
r_rigid_bond_restr 9.464
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2063
Nucleic Acid Atoms 0
Heterogen Atoms 134
Solvent Atoms 333

Software

Software
Software Name Purpose
REFMAC refinement
SCALA data scaling version: 3.3.20
PDB_EXTRACT data extraction version: 3.20
XDS data reduction
MOLREP phasing