X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details PEG 4000, MOPS, n-butanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.37 α = 90
b = 55.37 β = 90
c = 66.95 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV osmic blue optics 2002-05-23
Diffraction Radiation
Monochromator Protocol
NONE 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
2.04 40 100.0 0.054 -- -- 14.9 7504 7504 -- -3.0 --
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)
2.04 2.11 100.0 0.247 -- 10.7 14.6 728

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 2.04 40.0 -- 0.0 6675 6634 787 99.38 0.20083 0.20083 0.19537 0.24663 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 2.04 2.15 1054 103 478 0.215 0.271 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic temperature factors
Mean Isotropic B 27.792
Anisotropic B[1][1] -0.38
Anisotropic B[1][2] -0.19
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.57
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 5.33
r_scangle_it 7.764
r_dihedral_angle_1_deg 3.197
r_bond_refined_d 0.006
r_dihedral_angle_2_deg 16.329
r_xyhbond_nbd_refined 0.16
r_angle_refined_deg 1.172
r_symmetry_vdw_refined 0.302
r_nbd_refined 0.234
r_symmetry_hbond_refined 0.339
r_mcbond_it 1.843
r_mcangle_it 2.949
r_gen_planes_refined 0.003
r_chiral_restr 0.08
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 986
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 90

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement