X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.1
Temperature 293.0
Details PEG3350, citric acid, Bis-Tris propane, pH 4.1, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 153.53 α = 90
b = 114.26 β = 96.11
c = 68.41 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Osmic Blue 2008-05-12
Diffraction Radiation
Monochromator Protocol
Osmic Blue SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.54 -- --

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
2.01 50 99.3 -- 0.085 -- 9.9 -- 77785 -- -- 39.9
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)
2.01 2.08 93.0 -- 0.61 3.2 8.2 7283

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 2.01 50.0 -- 0.0 -- 77775 3916 99.5 -- 0.163 0.161 0.194 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 2.01 2.06 -- 290 5069 0.259 0.282 -- 93.44
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.358
Anisotropic B[1][1] 0.78
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.62
Anisotropic B[2][2] -1.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.84
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.299
r_scbond_it 2.947
r_mcangle_it 2.952
r_mcbond_it 2.079
r_gen_planes_refined 0.004
r_chiral_restr 0.072
r_dihedral_angle_4_deg 18.136
r_dihedral_angle_3_deg 13.364
r_dihedral_angle_2_deg 34.706
r_dihedral_angle_1_deg 5.598
r_angle_refined_deg 1.048
r_bond_refined_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.133
Luzzati ESD (R-Free Set) 0.124
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6162
Nucleic Acid Atoms 0
Heterogen Atoms 339
Solvent Atoms 735

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.5.0070 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 version: 5.5.0070 refinement
AMORE molecular replacement
HKL data processing