X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 292.0
Details 3.0 M ammonium sulfate, 0.1 M bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.8 α = 90
b = 116.43 β = 90
c = 36.99 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-10-19
Diffraction Radiation
Monochromator Protocol
Si - 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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 25 99.8 0.047 -- -- -- -- 16408 -- -- --
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 2.0 100.0 0.505 -- -- 5.3 --

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
PDB ENTRY 1DKZ 1.9 25.0 -- -- -- 15561 829 99.56 -- 0.2197 0.21606 0.29013 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 1.949 -- 50 1035 0.26 0.312 -- 99.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.626
Anisotropic B[1][1] -0.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.12
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.01
r_chiral_restr 0.126
r_dihedral_angle_4_deg 21.919
r_dihedral_angle_3_deg 16.809
r_dihedral_angle_2_deg 41.12
r_dihedral_angle_1_deg 5.639
r_angle_refined_deg 1.884
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1728
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 41

Software

Computing
Computing Package Purpose
marccd Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
refmac with PDBID 1DKZ Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
refmac version: with PDBID 1DKZ model building
marccd data collection