X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.4
Temperature 292.0
Details 20% glucose, 10-18% Peg8000, 200mM sodium acetate, MMT 100mM pH7.0-8.5, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.63 α = 90
b = 77.63 β = 90
c = 85.82 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 mirrors 2008-03-13
Diffraction Radiation
Monochromator Protocol
Osmic confocal multilayer mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E DW 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 54.8 91.9 0.078 -- -- 5.82 34425 31632 2.0 2.0 26.6
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)
2.0 2.07 51.3 0.309 -- 1.7 1.84 3406

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 2.0 25.89 -- 0.0 34431 29871 1613 91.44 0.18958 0.18958 0.18634 0.2491 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 2.0 2.052 -- 47 1139 0.316 0.517 -- 46.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.426
Anisotropic B[1][1] -1.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.53
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.105
r_dihedral_angle_4_deg 18.748
r_dihedral_angle_3_deg 15.494
r_dihedral_angle_2_deg 38.826
r_dihedral_angle_1_deg 6.495
r_angle_other_deg 0.864
r_angle_refined_deg 1.871
r_bond_other_d 0.001
r_bond_refined_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3457
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 252

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0032 refinement
AMoRE model building
CrystalClear data collection