X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 292.15
Details Morpheus Screen (Molecular Dimensions) A1 solution (0.1 M IMIDAZOLE/MES MONOHYDRATE (ACID) BUFFER PH 6.5, 10% W/V POLYETHYLENE GLYCOL 20000, 20% V/V PEG 500 MME, 0.03 M MAGNESIUM CHLORIDE HEXAHYDRATE AND 0.03 M CALCIUM CHLORIDE DIHYDRATE), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.97 α = 90
b = 81.52 β = 90
c = 107.78 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2015-09-12
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) 0.99999 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
2.1 50 99.9 0.041 -- -- 6.53 -- 30993 -- -- --
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)
-- -- 99.9 0.695 -- 3.35 6.79 --

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 2.1 43.68 -- -- -- 29440 1551 99.86 -- 0.19721 0.19541 0.23103 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 2.1 2.154 -- 113 2132 0.441 0.463 -- 99.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.376
Anisotropic B[1][1] -0.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.2
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_other 3.182
r_dihedral_angle_2_deg 38.733
r_scbond_it 3.183
r_dihedral_angle_4_deg 23.744
r_bond_refined_d 0.02
r_long_range_B_refined 7.808
r_dihedral_angle_3_deg 15.26
r_bond_other_d 0.011
r_gen_planes_other 0.009
r_mcbond_it 2.507
r_dihedral_angle_1_deg 7.443
r_mcbond_other 2.503
r_scangle_other 4.682
r_mcangle_other 3.722
r_gen_planes_refined 0.012
r_chiral_restr 0.115
r_long_range_B_other 7.808
r_mcangle_it 3.722
r_angle_refined_deg 1.956
r_angle_other_deg 1.954
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3784
Nucleic Acid Atoms 0
Heterogen Atoms 151
Solvent Atoms 112

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0107
XDS data reduction
XDS data scaling
MOLREP phasing