X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.3
Temperature 290.0
Details 60.8% MPD, 100MM NAHEPES PH 7.3- 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.81 α = 90
b = 59.15 β = 90
c = 61.46 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
CCD RIGAKU SATURN 944+ -- 2011-08-16
Diffraction Radiation
Monochromator Protocol
RIGAKU VARIAX HF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
1.7 50 99.2 0.035 -- -- 8.5 19769 19602 0.0 -3.0 29.13
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)
1.7 1.74 89.2 0.279 0.279 5.24 4.3 1417

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 1.7 42.62 -- 0.0 19769 18627 977 -- 0.156 0.156 0.155 0.171 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 1.7 1.74 -- 55 1111 0.193 0.223 -- 88.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic, TLS
Mean Isotropic B 20.36
Anisotropic B[1][1] 0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.115
r_dihedral_angle_4_deg 21.148
r_dihedral_angle_3_deg 10.921
r_dihedral_angle_2_deg 38.517
r_dihedral_angle_1_deg 5.828
r_angle_other_deg 0.993
r_angle_refined_deg 1.703
r_bond_other_d 0.001
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1184
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 202

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
direct refinement Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
direct version: refinement model building
StructureStudio data collection