X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 100 mM Tris, 16% PEG 8000, 100 mM NDSB-256, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.82 α = 90
b = 96.82 β = 90
c = 168.72 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-12-15
Diffraction Radiation
Monochromator Protocol
Synchrotron silicon crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.979 SSRL BL7-1

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
3.2 30 99.1 0.146 -- -- 3.8 13852 13727 0.0 0.0 --
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)
3.2 3.37 99.6 0.368 -- 2.0 4.0 1957

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
MOLECULAR REPLACEMENT 3.2 29.24 -- -- 13852 13001 678 100.0 -- 0.22903 0.22646 0.2767 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 3.2 3.282 -- 57 925 0.278 0.333 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.21
Anisotropic B[1][1] 0.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.64
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.83
r_scbond_it 0.469
r_mcangle_it 0.655
r_mcbond_it 0.361
r_symmetry_hbond_refined 0.103
r_bond_refined_d 0.006
r_angle_refined_deg 1.005
r_dihedral_angle_1_deg 5.179
r_dihedral_angle_2_deg 34.478
r_dihedral_angle_3_deg 18.455
r_dihedral_angle_4_deg 18.066
r_chiral_restr 0.072
r_gen_planes_refined 0.002
r_nbd_refined 0.193
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.129
r_symmetry_vdw_refined 0.186
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4174
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 0

Software

Computing
Computing Package Purpose
Blu-Ice Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Refmac Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
Refmac model building
Blu-Ice data collection