X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 1 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5, cryoprotectant: Paratone N, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.64 α = 90
b = 96.64 β = 90
c = 92.03 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE -- Varimax 2008-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --

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
2.19 19.05 99.2 0.061 -- -- -- -- 24866 -- -3.0 38.113
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)
2.19 2.25 91.4 0.429 -- 3.84 -- --

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 2.19 19.047 -- 0.0 -- 24829 1226 99.06 -- 0.1466 0.1439 0.1987 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 2.19 2.248 -- -- 1638 0.222 -- -- 88.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.6047
Anisotropic B[1][1] -1.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.65
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.691
r_gen_planes_refined 0.008
r_mcbond_other 0.252
r_bond_refined_d 0.022
r_gen_planes_other 0.001
r_angle_other_deg 1.036
r_dihedral_angle_4_deg 22.743
r_dihedral_angle_2_deg 37.675
r_dihedral_angle_1_deg 7.04
r_mcbond_it 0.915
r_scangle_it 3.873
r_bond_other_d 0.001
r_mcangle_it 1.629
r_chiral_restr 0.109
r_angle_refined_deg 1.88
r_dihedral_angle_3_deg 17.929
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3518
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 104

Software

Software
Software Name Purpose
XSCALE data scaling
REFMAC refinement version: 5.5.0102
PDB_EXTRACT data extraction version: 3.10
XDS data reduction
PHASER phasing