X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 298.0
Details 0.8M AMMONIUM SULPHATE, 0.1M CITRATE, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.24 α = 90
b = 93.4 β = 90
c = 180.74 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2004-05-23
Diffraction Radiation
Monochromator Protocol
SI SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.9 SPring-8 BL26B2

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
1.48 41.49 96.7 0.073 -- -- 6.63 111799 111799 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)
1.48 1.53 98.9 0.288 -- 5.0 5.26 11283

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 1.48 41.49 -- 0.0 111795 111795 5592 96.66 0.169 0.169 0.168 0.19 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 1.48 1.518 8333 402 7931 0.253 0.286 -- 98.62
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.577
Anisotropic B[1][1] -0.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.37
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.212
r_dihedral_angle_1_deg 5.73
r_gen_planes_refined 0.005
r_angle_refined_deg 1.447
r_mcbond_it 0.481
r_mcangle_it 0.745
r_dihedral_angle_4_deg 13.548
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.146
r_nbd_refined 0.199
r_chiral_restr 0.085
r_dihedral_angle_3_deg 12.394
r_scangle_it 1.414
r_symmetry_hbond_refined 0.256
r_dihedral_angle_2_deg 32.392
r_nbtor_refined 0.307
r_scbond_it 1.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4186
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 498

Software

Software
Software Name Purpose
d*TREK data scaling version: 8.0SSI
MOLREP phasing
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 1.701
BBS data reduction