X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details The protein concentration was adjusted to 10 mg/ml. The protein solution was supplemented with cyclosporin A at a molar ratio of 2:1 and mixed with the reservoir solution containing 2.4 M sodium malonate, pH 7.0.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.58 α = 90
b = 86.58 β = 90
c = 119.52 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2017-06-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 1.0332 PETRA III, EMBL c/o DESY P14 (MX2)

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
1.98 70.12 99.8 -- 0.101 6.1 5.6 -- 16197 -- -- --
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)
1.98 2.08 100.0 0.466 0.466 1.6 5.9 --

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 1.98 70.12 -- 0.0 -- 15368 813 99.92 -- 0.1856 0.1838 0.2231 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 1.98 2.031 -- 77 1092 0.338 0.368 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.262
Anisotropic B[1][1] 1.68
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.36
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 2.011
r_chiral_restr 0.154
r_dihedral_angle_3_deg 15.968
r_bond_refined_d 0.018
r_dihedral_angle_4_deg 13.449
r_bond_other_d 0.002
r_gen_planes_other 0.002
r_dihedral_angle_1_deg 6.389
r_gen_planes_refined 0.009
r_angle_other_deg 1.157
r_dihedral_angle_2_deg 38.626
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1279
Nucleic Acid Atoms 0
Heterogen Atoms 93
Solvent Atoms 50

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.22
MOLREP phasing version: 11.1.00
REFMAC refinement version: 5.8.0103
PDB_EXTRACT data extraction version: 3.24
iMOSFLM data reduction version: 7.1.1