X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.5 α = 90
b = 84.23 β = 90
c = 89.82 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 MARRESEARCH -- 2008-07-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA

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
2.37 38.12 94.7 0.088 -- -- 5.1 -- 12709 -- 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)
2.37 2.57 94.5 0.788 -- -- 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
-- 2.37 38.12 -- 0.0 -- 12074 608 95.02 -- 0.2409 0.2385 0.2846 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 2.37 2.431 -- 39 805 0.335 0.432 -- 95.37
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.765
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.27
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.336
r_nbd_refined 0.193
r_gen_planes_other 0.003
r_gen_planes_refined 0.004
r_chiral_restr 0.062
r_dihedral_angle_4_deg 18.692
r_dihedral_angle_3_deg 14.944
r_dihedral_angle_2_deg 34.58
r_dihedral_angle_1_deg 5.742
r_angle_other_deg 0.72
r_angle_refined_deg 1.045
r_bond_other_d 0.001
r_bond_refined_d 0.008
r_nbd_other 0.176
r_nbtor_refined 0.181
r_nbtor_other 0.083
r_xyhbond_nbd_refined 0.158
r_xyhbond_nbd_other 0.029
r_symmetry_vdw_refined 0.09
r_symmetry_vdw_other 0.197
r_symmetry_hbond_refined 0.138
r_mcbond_it 1.626
r_mcbond_other 0.335
r_mcangle_it 2.066
r_scbond_it 3.234
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2121
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 21

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.2.0005 refinement