X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 291.0
Details PEG 3350, potassium phosphate, magnesium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.57 α = 90
b = 67.57 β = 90
c = 193.37 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2003-05-16
Diffraction Radiation
Monochromator Protocol
Rh coated silica SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX14.2 0.975 SRS PX14.2

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
1.3 25 99.9 -- 0.062 -- 12.08 42313 n/a -- -- 13.695
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)
1.3 1.32 100.0 -- 0.586 4.32 11.3 2080

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 1.3 23.33 -- 0.0 -- 42303 2058 99.75 0.1807 0.1807 0.1798 0.1954 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 1.298 1.332 2906 148 3054 0.19 0.207 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 14.373
Anisotropic B[1][1] -0.34
Anisotropic B[1][2] -0.17
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.51
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.954
r_sphericity_free 4.108
r_rigid_bond_restr 1.291
r_scangle_it 3.55
r_scbond_it 2.258
r_mcangle_it 1.97
r_mcbond_it 1.244
r_symmetry_hbond_refined 0.293
r_symmetry_vdw_other 0.347
r_symmetry_vdw_refined 0.344
r_bond_refined_d 0.01
r_bond_other_d 0.004
r_angle_refined_deg 1.437
r_angle_other_deg 1.05
r_dihedral_angle_1_deg 6.524
r_chiral_restr 0.099
r_gen_planes_refined 0.007
r_gen_planes_other 0.01
r_nbd_refined 0.23
r_nbd_other 0.278
r_nbtor_other 0.084
r_xyhbond_nbd_refined 0.266
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.05
Luzzati ESD (R-Free Set) 0.046
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 950
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 267

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement