X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 0.1 M Hepes (pH 7.5), 1 M succinic Acid, 1% (w/v) PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.13 α = 90
b = 120.83 β = 90
c = 122.85 γ = 90
Symmetry
Space Group I 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 -- 2009-01-01
Diffraction Radiation
Monochromator Protocol
VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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
1.72 85.7 94.3 -- 0.051 -- 3.5 89172 84134 -3.0 -3.0 --

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
-- 1.72 85.69 -- 0.0 -- -- 4474 94.35 0.2004 0.2004 0.1985 0.2346 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 1.72 1.765 -- 287 5447 0.302 0.327 -- 83.67
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.9314
Anisotropic B[1][1] 2.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.82
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 17.036
r_bond_refined_d 0.031
r_angle_refined_deg 2.595
r_dihedral_angle_1_deg 6.476
r_dihedral_angle_2_deg 30.761
r_dihedral_angle_3_deg 14.788
r_dihedral_angle_4_deg 20.403
r_chiral_restr 0.201
r_gen_planes_refined 0.013
r_mcbond_it 1.566
r_mcangle_it 2.593
r_scbond_it 5.525
r_scangle_it 8.657
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4039
Nucleic Acid Atoms 0
Heterogen Atoms 71
Solvent Atoms 470

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement