X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Micro Batch
pH 7.5
Temperature 293.0
Details Lithium sulfate, HEPES, dithiotreitol, pH 7.5, MICRO BATCH, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.89 α = 90
b = 146.89 β = 90
c = 381.68 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2001-06-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8452 EMBL/DESY, HAMBURG BW7B

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
3.4 20 92.5 0.089 -- -- -- -- 18266 -- -3.0 88.3
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)
3.4 3.52 79.9 0.383 -- 2.51 -- 1713

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 3.4 6.0 -- 0.0 -- 15805 858 92.52 -- 0.29788 0.29675 0.31895 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 3.4 3.459 -- 42 775 0.316 0.322 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 134.533
Anisotropic B[1][1] -2.33
Anisotropic B[1][2] -1.16
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.49
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 1.859
r_nbd_other 0.289
r_nbd_refined 0.287
r_gen_planes_other 0.004
r_gen_planes_refined 0.007
r_chiral_restr 0.103
r_dihedral_angle_3_deg 20.954
r_dihedral_angle_1_deg 2.536
r_angle_other_deg 1.052
r_angle_refined_deg 1.995
r_bond_other_d 0.003
r_bond_refined_d 0.025
r_xyhbond_nbd_refined 0.191
r_xyhbond_nbd_other 0.154
r_symmetry_vdw_refined 0.298
r_symmetry_vdw_other 0.393
r_symmetry_hbond_refined 0.229
r_mcbond_it 2.891
r_mcangle_it 5.371
r_scbond_it 5.781
r_scangle_it 9.927
r_rigid_bond_restr 3.621
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7187
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building