X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details PEG8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.07 α = 90
b = 110.02 β = 90
c = 139.06 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
CCD ADSC QUANTUM 4 -- 2004-08-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.9186 CHESS F1

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
1.27 30 95.9 0.083 -- -- 5.8 278149 266666 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)
1.27 1.3 73.1 0.26 -- 5.1 2.9 12623

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 1.27 29.36 -- 0.0 277995 262677 5985 94.49 -- 0.148 0.148 0.173 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 1.27 1.303 -- 328 13722 0.188 0.239 -- 68.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.197
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.308
r_xyhbond_nbd_refined 0.116
r_symmetry_hbond_refined 0.136
r_bond_refined_d 0.01
r_angle_refined_deg 1.348
r_chiral_restr 0.09
r_gen_planes_refined 0.007
r_symmetry_vdw_refined 0.194
r_scbond_it 2.435
r_scangle_it 3.329
r_dihedral_angle_1_deg 6.063
r_mcangle_it 1.761
r_rigid_bond_restr 1.639
r_dihedral_angle_4_deg 18.906
r_sphericity_bonded 3.746
r_mcbond_it 1.203
r_nbd_refined 0.195
r_dihedral_angle_3_deg 11.745
r_dihedral_angle_2_deg 36.836
r_sphericity_free 4.799
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8196
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 1364

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
ADSC data collection version: Quantum
HKL-2000 data reduction
SADABS data scaling
CNS phasing