X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 277.0
Details PEG4000, Tris-HCl, MgCl2, MPD, NaNO2, pH 8.5, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.11 α = 90
b = 133.11 β = 90
c = 77.8 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 Vertical and horizontal Silicon single crystal mirrors 2008-12-07
Diffraction Radiation
Monochromator Protocol
Si(111) Double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A

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
1.4 50 97.4 0.118 0.118 -- 6.5 134915 134915 0.0 0.0 21.7
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)
1.4 1.45 77.2 0.404 -- 2.52 6.0 10563

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 1.4 29.25 0.0 0.0 134844 134844 6773 100.0 0.1757 0.1757 0.175 0.1892 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 1.403 1.44 9365 462 8903 0.268 0.274 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.8876
Anisotropic B[1][1] -0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.62
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.096
r_angle_refined_deg 1.217
r_mcangle_it 0.886
r_symmetry_vdw_refined 0.144
r_symmetry_hbond_refined 0.118
r_metal_ion_refined 0.101
r_bond_refined_d 0.007
r_dihedral_angle_1_deg 5.982
r_mcbond_it 0.455
r_scbond_it 1.51
r_gen_planes_refined 0.005
r_nbd_refined 0.202
r_chiral_restr 0.082
r_dihedral_angle_2_deg 31.399
r_dihedral_angle_3_deg 11.86
r_nbtor_refined 0.306
r_dihedral_angle_4_deg 13.163
r_scangle_it 2.471
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.141
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4246
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 922

Software

Software
Software Name Purpose
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
ADSC data collection version: Quantum
HKL-2000 data reduction