X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Details pH 7.20, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.78 α = 72.6
b = 64.23 β = 73.86
c = 64.54 γ = 73.56
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MACSCIENCE MIRRORS 2000-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR591 1.5418 -- --

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 30 95.4 -- 0.082 -- 2.182 32375 30886 -- -3.0 27.2
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 2.34 92.7 -- 0.173 4.6 -- --

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
MOLECULAR REPLACEMENT 2.3 19.14 -- 0.0 -- 29257 1583 100.0 -- 0.15412 0.15127 0.20601 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 -- -- -- -- 0.159 0.228 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model iostropic
Mean Isotropic B 15.691
Anisotropic B[1][1] -0.22
Anisotropic B[1][2] 0.09
Anisotropic B[1][3] -0.49
Anisotropic B[2][2] 0.38
Anisotropic B[2][3] -0.14
Anisotropic B[3][3] 0.14
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.912
r_scbond_it 1.787
r_mcangle_it 1.011
r_nbd_refined 0.226
r_gen_planes_refined 0.005
r_chiral_restr 0.086
r_dihedral_angle_3_deg 17.128
r_dihedral_angle_1_deg 3.501
r_angle_refined_deg 1.267
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.139
r_metal_ion_refined 0.16
r_symmetry_vdw_refined 0.182
r_symmetry_hbond_refined 0.173
r_mcbond_it 0.524
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6074
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 475

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK, CCP4 (TRUNCATE) Data Reduction (data scaling)
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
REFMAC model building
SCALEPACK/TRUNCATE data reduction
DENZO data collection