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_dihedral_angle_4_deg 21.148
r_bond_other_d 0.001
r_dihedral_angle_1_deg 5.828
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 10.921
r_angle_other_deg 0.993
r_bond_refined_d 0.016
r_dihedral_angle_2_deg 38.517
r_chiral_restr 0.115
r_angle_refined_deg 1.703
r_gen_planes_refined 0.008
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

Software
Software Name Purpose
StructureStudio data collection
direct model building version: refinement
REFMAC refinement version: 5.6.0117
XDS data reduction
XSCALE data scaling
direct phasing version: refinement