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 = 67.07 α = 90
b = 67.07 β = 90
c = 46.91 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 -- 2011-04-26
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
1.71 27.28 97.0 -- 0.045 -- 5.8 13044 13044 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)
1.7 1.79 85.9 0.264 0.264 2.8 5.4 1668

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 1.71 27.28 -- 0.0 13019 13019 613 98.68 0.2064 0.2064 0.2045 0.2461 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 1.706 1.75 -- 47 882 0.385 0.474 -- 96.27
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.6901
Anisotropic B[1][1] 0.88
Anisotropic B[1][2] 0.44
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.32
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.008
r_scbond_it 2.542
r_mcangle_it 1.511
r_mcbond_it 0.887
r_gen_planes_refined 0.006
r_chiral_restr 0.109
r_dihedral_angle_4_deg 15.648
r_dihedral_angle_3_deg 13.353
r_dihedral_angle_2_deg 26.637
r_dihedral_angle_1_deg 6.637
r_angle_refined_deg 1.536
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 867
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 82

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