X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 7.1
Temperature 277.0
Details 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.46 α = 90
b = 60.46 β = 90
c = 96 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2006-11-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
1.8 52.34 99.7 -- -- -- -- 19492 19434 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)
1.798 1.84 98.9 -- -- -- -- --

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
-- 1.798 52.34 -- 0.0 19464 19408 994 99.71 0.188 0.188 0.187 0.212 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 1.798 1.844 1904 75 1314 0.278 0.302 -- 98.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.548
Anisotropic B[1][1] 0.12
Anisotropic B[1][2] 0.06
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.19
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 32.478
r_nbtor_refined 0.303
r_symmetry_hbond_refined 0.207
r_mcangle_it 1.236
r_scbond_it 2.173
r_nbd_refined 0.197
r_chiral_restr 0.088
r_mcbond_it 0.786
r_scangle_it 3.19
r_angle_refined_deg 1.249
r_dihedral_angle_3_deg 13.223
r_bond_refined_d 0.014
r_gen_planes_refined 0.005
r_dihedral_angle_1_deg 5.25
r_xyhbond_nbd_refined 0.152
r_dihedral_angle_4_deg 16.87
r_symmetry_vdw_refined 0.183
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1285
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 213

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.000
HKL-3000 data collection
DENZO data reduction
SCALEPACK data scaling
HKL-3000 data scaling
REFMAC phasing version: 5.2