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_scangle_it 3.092
r_scbond_it 2.037
r_mcangle_it 1.383
r_mcbond_other 0.241
r_bond_refined_d 0.017
r_bond_other_d 0.001
r_angle_refined_deg 1.505
r_angle_other_deg 0.981
r_dihedral_angle_1_deg 7.214
r_dihedral_angle_2_deg 31.498
r_dihedral_angle_3_deg 12.306
r_dihedral_angle_4_deg 8.551
r_chiral_restr 0.095
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_mcbond_it 0.818
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

Computing
Computing Package Purpose
MAR345dtb Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.5.0102 refinement
Phaser version: 2.1.4 molecular replacement
SCALA version: 3.3.15 data reduction
Mosflm data collection