X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details Na2SO4, Bis-Tris propane, PEG3350, Ethylene Glycol, DMSO, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.55 α = 90
b = 99.55 β = 90
c = 80.06 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 RIGAKU RAXIS HTC Multi-layer VariMax HR 2004-10-21
Diffraction Radiation
Monochromator Protocol
Copper K-alpha SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E 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
1.8 86.07 99.5 0.068 0.068 -- 6.3 41697 41578 0.0 0.0 30.1
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)
1.8 1.9 98.2 0.781 0.781 1.5 4.1 5939

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 1.8 58.67 0.0 0.0 47251 39589 2136 58.67 0.18164 0.18164 0.17999 0.21336 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 1.8 1.847 -- 168 2909 0.28 0.322 -- 99.26
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.881
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.094
r_scbond_it 2.586
r_mcangle_it 1.648
r_nbd_refined 0.201
r_gen_planes_refined 0.007
r_chiral_restr 0.112
r_dihedral_angle_4_deg 18.091
r_dihedral_angle_3_deg 13.182
r_dihedral_angle_2_deg 34.6
r_dihedral_angle_1_deg 5.769
r_angle_refined_deg 1.914
r_bond_refined_d 0.018
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.16
r_symmetry_vdw_refined 0.108
r_symmetry_hbond_refined 0.173
r_mcbond_it 1.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2213
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 242

Software

Computing
Computing Package Purpose
CRYSTALCLEAR (MSC/RIGAKU) Data Reduction (intensity integration)
CRYSTALCLEAR (MSC/RIGAKU) Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement