X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 293.0
Details 10% (v/v) 2-propanol, 3% glycerol, 100 mM HEPES, pH 7.8, and 11% (w/v) PEG 4,000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.25 α = 90
b = 38.25 β = 90
c = 186.96 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2015-07-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54 -- --

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
2.08 24.81 98.06 -- -- -- 6.4 -- 9086 -- -- --
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)
2.08 2.154 87.88 0.1861 -- 5.39 2.7 --

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 2.08 24.81 -- -- -- 8650 435 97.98 -- 0.15823 0.15642 0.19421 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 2.08 2.134 -- 34 579 0.197 0.204 -- 85.85
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.113
Anisotropic B[1][1] 0.26
Anisotropic B[1][2] 0.26
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.83
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.006
r_angle_refined_deg 1.253
r_bond_other_d 0.001
r_dihedral_angle_2_deg 35.934
r_dihedral_angle_1_deg 5.619
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 12.313
r_chiral_restr 0.199
r_angle_other_deg 0.913
r_gen_planes_refined 0.004
r_dihedral_angle_4_deg 11.445
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1334
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 88

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0029
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing