X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 291.0
Details 1M Sodium Potassium Phosphate pH 7.4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.94 α = 90
b = 64.94 β = 90
c = 158.39 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2016-06-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALBA BEAMLINE XALOC 0.979490 ALBA XALOC

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
2.45 60.08 96.1 0.04 -- -- 16.7 -- 12717 -- -- --
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)
2.45 2.55 -- 0.63 -- 3.4 17.7 --

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 2.45 60.08 -- -- -- 12040 621 96.16 -- 0.1977 0.19668 0.21724 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 2.45 2.514 -- 42 909 0.337 0.375 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.307
Anisotropic B[1][1] 2.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.11
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.009
r_scbond_it 3.916
r_chiral_restr 0.084
r_dihedral_angle_2_deg 34.302
r_mcangle_it 5.549
r_scbond_other 3.914
r_angle_refined_deg 1.364
r_dihedral_angle_3_deg 15.418
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 20.254
r_dihedral_angle_1_deg 6.155
r_long_range_B_refined 9.265
r_mcbond_it 3.41
r_mcangle_other 5.546
r_angle_other_deg 0.974
r_bond_other_d 0.002
r_mcbond_other 3.409
r_long_range_B_other 9.268
r_scangle_other 6.522
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1310
Nucleic Acid Atoms 84
Heterogen Atoms 16
Solvent Atoms 38

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
XDS data reduction
Aimless data scaling
Coot model building
MOLREP phasing