X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.2
Details pH 7.2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.65 α = 90
b = 165.94 β = 90
c = 79.22 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC YALE MIRRORS 1998-07-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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 30 97.9 0.044 -- -- 8.0 -- 54052 -- -3.0 --
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)
2.0 2.07 93.9 0.214 -- 7.77 4.0 --

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
DIFFERENCE FOURIER 2.0 30.0 -- -- -- 49955 2681 97.43 -- 0.17918 0.1773 0.21445 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 2.0 2.052 -- -- 3312 0.207 0.25 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.821
Anisotropic B[1][1] 1.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.04
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.005
r_xyhbond_nbd_refined 0.118
r_mcbond_it 1.67
r_symmetry_vdw_other 0.234
r_angle_refined_deg 2.136
r_angle_other_deg 1.197
r_nbtor_other 0.083
r_bond_other_d 0.002
r_dihedral_angle_3_deg 19.715
r_chiral_restr 0.121
r_symmetry_hbond_refined 0.206
r_bond_refined_d 0.013
r_nbd_refined 0.228
r_nbd_other 0.221
r_gen_planes_refined 0.008
r_mcangle_it 3.016
r_dihedral_angle_1_deg 3.964
r_scbond_it 3.535
r_symmetry_vdw_refined 0.181
r_scangle_it 5.5
r_xyhbond_nbd_other 0.345
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4882
Nucleic Acid Atoms 0
Heterogen Atoms 140
Solvent Atoms 540

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CCP4 model building
REFMAC refinement version: 5.0
CCP4 phasing