X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 298.0
Details 20-30% PEG3000, 10 mM CaCl2, 50 mM CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.04 α = 90
b = 74.02 β = 90
c = 76.7 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2001-08-15
Diffraction Radiation
Monochromator Protocol
crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-BM 1.0 APS 17-BM

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
2.3 40 92.7 0.062 0.062 -- 3.7 15856 15856 -1.5 -3.0 48.4
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)
2.3 2.38 63.6 0.449 0.449 2.1 3.0 1066

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
FOURIER SYNTHESIS 2.3 37.01 -- -- -- 15033 780 92.81 0.21666 0.21666 0.21431 0.26185 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 2.3 2.359 -- 47 722 0.28 0.307 -- 62.52
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained individual
Mean Isotropic B 35.879
Anisotropic B[1][1] -1.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.02
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.202
r_dihedral_angle_4_deg 19.455
r_nbd_other 0.19
r_bond_refined_d 0.009
r_nbtor_other 0.088
r_symmetry_vdw_other 0.223
r_symmetry_hbond_refined 0.166
r_mcbond_other 0.078
r_angle_other_deg 0.885
r_dihedral_angle_3_deg 17.393
r_gen_planes_refined 0.004
r_bond_other_d 0.001
r_nbtor_refined 0.184
r_dihedral_angle_1_deg 5.884
r_scbond_it 1.055
r_scangle_it 1.538
r_chiral_restr 0.07
r_gen_planes_other 0.001
r_xyhbond_nbd_refined 0.158
r_angle_refined_deg 1.279
r_dihedral_angle_2_deg 34.674
r_mcbond_it 0.633
r_symmetry_vdw_refined 0.134
r_mcangle_it 0.715
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2665
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 166

Software

Software
Software Name Purpose
HKL-2000 data collection
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling