X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.6
Temperature 298.0
Details 20% PEG 4000, 50 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE, 5 MM DTT, PH 4.7, TRANSFERRED TO PH 7.6 FOR SOAKING, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.11 α = 90
b = 106.39 β = 90
c = 126.73 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2006-07-27
Diffraction Radiation
Monochromator Protocol
OSMIC MIRRORS 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
2.4 29.12 92.48 0.12 -- -- 3.3 42702 42702 0.0 -- 38.6
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)
2.4 2.42 94.0 -- -- 4.4 -- 1038

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 2.4 29.12 -- 0.0 42702 40579 2121 92.48 0.24033 0.24033 0.23728 0.29974 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 2.4 2.462 -- 171 2935 0.298 0.368 -- 93.44
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 45.224
Anisotropic B[1][1] -1.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.5
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 35.083
r_nbd_refined 0.197
r_symmetry_vdw_refined 0.198
r_dihedral_angle_3_deg 15.492
r_mcangle_it 1.711
r_dihedral_angle_4_deg 15.638
r_symmetry_hbond_refined 0.152
r_gen_planes_refined 0.003
r_scbond_it 1.456
r_xyhbond_nbd_refined 0.149
r_angle_refined_deg 1.098
r_dihedral_angle_1_deg 5.566
r_mcbond_it 1.08
r_chiral_restr 0.068
r_scangle_it 2.042
r_bond_refined_d 0.008
r_nbtor_refined 0.293
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8668
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 209

Software

Software
Software Name Purpose
CrystalClear data collection
EPMR phasing
REFMAC refinement version: 5.2
HKL-2000 data reduction
HKL-2000 data scaling