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 = 116.5 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 289
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
1.93 91.29 99.9 -- 0.047 -- -- -- 74225 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)
1.93 1.96 99.9 -- 0.425 4.2 4.4 --

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 1.93 30.0 -- 0.0 -- 74225 3734 99.91 -- 0.176 0.175 0.207 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 1.93 1.98 -- 287 5116 0.226 0.255 -- 99.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.644
Anisotropic B[1][1] 0.59
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] -1.18
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.188
r_nbtor_refined 0.303
r_scangle_it 2.778
r_angle_refined_deg 1.09
r_dihedral_angle_3_deg 14.593
r_symmetry_vdw_refined 0.122
r_chiral_restr 0.081
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.112
r_dihedral_angle_4_deg 17.937
r_scbond_it 1.69
r_dihedral_angle_1_deg 5.24
r_mcbond_it 0.603
r_gen_planes_refined 0.003
r_dihedral_angle_2_deg 34.402
r_mcangle_it 1.134
r_symmetry_hbond_refined 0.102
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6624
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 388

Software

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