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_scangle_it 3.873
r_scbond_it 2.691
r_mcangle_it 1.629
r_mcbond_other 0.252
r_bond_refined_d 0.022
r_bond_other_d 0.001
r_angle_refined_deg 1.88
r_angle_other_deg 1.036
r_dihedral_angle_1_deg 7.04
r_dihedral_angle_2_deg 37.675
r_dihedral_angle_3_deg 17.929
r_dihedral_angle_4_deg 22.743
r_chiral_restr 0.109
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_mcbond_it 0.915
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.5.0102 refinement
Xscale data reduction