X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.6
Temperature 277.0
Details 0.1 M Tris-HCl, 18% PEG6000, 0.2 M lithium chloride, pH 7.6, vapor diffusion, sitting drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.98 α = 90
b = 66.98 β = 90
c = 46.76 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 114
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2011-04-27
Diffraction Radiation
Monochromator Protocol
Graded multilayer (osmic) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.8 58.01 99.6 -- 0.038 -- 5.9 11161 11161 0.0 0.0 --
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)
1.8 1.9 100.0 0.267 0.267 2.9 5.8 1641

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 1.8 58.006 -- 0.0 11144 11144 530 99.56 0.2072 0.2072 0.2052 0.2451 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 1.801 1.847 -- 45 790 0.281 0.297 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.1007
Anisotropic B[1][1] 0.81
Anisotropic B[1][2] 0.4
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.21
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.005
r_scbond_it 2.478
r_mcangle_it 1.423
r_mcbond_it 0.809
r_gen_planes_refined 0.006
r_chiral_restr 0.102
r_dihedral_angle_4_deg 17.415
r_dihedral_angle_3_deg 14.148
r_dihedral_angle_2_deg 26.401
r_dihedral_angle_1_deg 6.204
r_angle_refined_deg 1.482
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 867
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 63

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA version: 3.3.16 data reduction
Mosflm data collection