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 = 129.13 α = 90
b = 129.13 β = 90
c = 117.01 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
2 99 97.5 0.051 -- -- 5.0 -- 65604 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)
2.0 2.03 98.3 0.493 -- 2.2 4.8 3272

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 2.0 49.27 -- 0.0 -- 65585 3319 97.56 -- 0.185 0.184 0.215 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 2.051 -- 254 4573 0.243 0.281 -- 97.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.109
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.05
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 19.797
r_scangle_it 2.889
r_mcbond_it 0.654
r_angle_refined_deg 1.182
r_symmetry_hbond_refined 0.123
r_gen_planes_refined 0.004
r_dihedral_angle_2_deg 34.244
r_nbtor_refined 0.304
r_chiral_restr 0.086
r_xyhbond_nbd_refined 0.119
r_symmetry_vdw_refined 0.147
r_nbd_refined 0.189
r_bond_refined_d 0.01
r_dihedral_angle_3_deg 15.193
r_dihedral_angle_1_deg 5.437
r_mcangle_it 1.222
r_scbond_it 1.768
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6597
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 293

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