X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 6.7
Temperature 289.0
Details 10MM BES BUFFER, 3MM DDT, pH 6.7, small tubes, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 129.1 α = 90
b = 129.1 β = 90
c = 116.56 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2009-07-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, Hamburg X13

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
1.9 91.29 98.7 -- 0.044 -- 5.0 -- 76656 0.0 -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)
1.9 1.93 99.9 -- 0.444 41.0 5.1 --

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
FOURIER SYNTHESIS 1.9 30.0 -- 0.0 -- 76656 3855 98.57 -- 0.183 0.182 0.211 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 1.9 1.95 -- 294 5332 0.231 0.281 -- 99.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.621
Anisotropic B[1][1] 0.71
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.43
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.161
r_mcbond_it 0.7
r_mcangle_it 1.158
r_dihedral_angle_4_deg 18.4
r_gen_planes_refined 0.003
r_nbd_refined 0.187
r_dihedral_angle_2_deg 35.302
r_scbond_it 1.74
r_scangle_it 2.799
r_chiral_restr 0.082
r_dihedral_angle_3_deg 14.298
r_nbtor_refined 0.303
r_bond_refined_d 0.009
r_dihedral_angle_1_deg 5.311
r_symmetry_hbond_refined 0.113
r_xyhbond_nbd_refined 0.123
r_angle_refined_deg 1.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6613
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 348

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.3.0037
PDB_EXTRACT data extraction version: 3.005
DNA data collection
REFMAC phasing