X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details 30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL, pH 8.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.91 α = 115.18
b = 74.68 β = 93.14
c = 87.59 γ = 109.33
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC MIRRORS 2001-07-13
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 -- ESRF BM14

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 20 97.6 0.073 -- -- 4.2 -- 235655 -- -- --
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 1.56 90.4 0.345 -- 1.6 3.6 --

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
SIRAS 1.48 20.0 -- -- -- 233691 1894 96.8 -- 0.133 0.133 0.168 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 1.52 -- 134 14735 0.203 0.284 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.86
Anisotropic B[1][1] 0.46
Anisotropic B[1][2] 0.11
Anisotropic B[1][3] -0.16
Anisotropic B[2][2] -0.1
Anisotropic B[2][3] -0.3
Anisotropic B[3][3] -0.56
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.724
r_scbond_it 2.577
r_mcangle_it 1.833
r_mcbond_it 1.271
r_nbd_refined 0.251
r_gen_planes_other 0.002
r_gen_planes_refined 0.009
r_chiral_restr 0.122
r_dihedral_angle_3_deg 16.102
r_dihedral_angle_1_deg 4.919
r_angle_other_deg 2.019
r_angle_refined_deg 1.589
r_bond_other_d 0.001
r_bond_refined_d 0.016
r_nbd_other 0.207
r_nbtor_other 0.194
r_xyhbond_nbd_refined 0.151
r_xyhbond_nbd_other 0.082
r_metal_ion_refined 0.123
r_symmetry_vdw_refined 0.183
r_symmetry_vdw_other 0.211
r_symmetry_hbond_refined 0.213
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11376
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 1766

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement