X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 2 uL 0.1 M sodium phosphate, pH 5.5, 10% w/v PEG6000 + 2 uL 100 U/mL human insulin (Novolin R, lot # XS60393), cryoprotectant: mother liquor + 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.17 α = 90
b = 82.17 β = 90
c = 33.73 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2009-12-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU ULTRAX 18 1.54179 -- --

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
1.68 41.08 97.4 -- 0.071 -- 5.6 9605 9605 -- -- --
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)
1.679 1.76 86.1 0.344 0.344 2.1 5.0 1244

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 1.679 41.08 -- 0.0 -- 9605 462 99.29 -- 0.2162 0.2137 0.2644 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 1.679 1.722 -- 26 644 0.221 0.298 -- 98.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.9974
Anisotropic B[1][1] 0.12
Anisotropic B[1][2] 0.06
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.18
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_scangle_it 3.092
r_bond_other_d 0.001
r_scbond_it 2.037
r_dihedral_angle_4_deg 8.551
r_mcangle_it 1.383
r_angle_refined_deg 1.505
r_angle_other_deg 0.981
r_chiral_restr 0.095
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 7.214
r_dihedral_angle_3_deg 12.306
r_dihedral_angle_2_deg 31.498
r_mcbond_it 0.818
r_mcbond_other 0.241
r_bond_refined_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 804
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 142

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.15
PHASER phasing version: 2.1.4
REFMAC refinement version: 5.5.0102
PDB_EXTRACT data extraction version: 3.11
MAR345dtb data collection