X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 295.0
Details KSCN, PEG4000, NaAcetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57 α = 90
b = 70.08 β = 90
c = 97.96 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm Multilayer mirror 2009-04-01
Diffraction Radiation
Monochromator Protocol
Bent diamond crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-5 0.90778 MAX II I911-5

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
1.6 20 92.5 0.056 -- -- 4.7 -- 50801 -- -- --
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)
1.6 1.7 85.0 0.38 -- 4.45 4.7 7327

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
Solved with MAD and refined against native data set 1.6 15.0 -- -- 52013 49365 2648 99.2 0.229 0.18412 0.1816 0.23321 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 1.6 1.641 3560 213 3560 0.225 0.309 -- 99.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.389
Anisotropic B[1][1] -0.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.83
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.27
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 15.384
r_sphericity_free 18.563
r_rigid_bond_restr 3.519
r_bond_refined_d 0.003
r_angle_refined_deg 0.929
r_dihedral_angle_1_deg 3.576
r_dihedral_angle_2_deg 29.983
r_dihedral_angle_3_deg 10.868
r_dihedral_angle_4_deg 12.533
r_chiral_restr 0.065
r_gen_planes_refined 0.004
r_mcbond_it 3.065
r_mcangle_it 4.709
r_scbond_it 5.002
r_scangle_it 7.659
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3207
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 392

Software

Computing
Computing Package Purpose
mar Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
Phenix Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0072 refinement
Phenix model building
mar data collection