X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 291.0
Details 2 uL 0.1 M sodium phosphate, pH 5.5, 10% w/v PEG6000 + 2 uL 100 U/mL human insulin (Humulin R, lot # A 405936), cryoprotectant: mother liquor + 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.12 α = 90
b = 82.12 β = 90
c = 33.8 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 -- --
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 41.06 98.1 -- 0.064 -- 5.9 9692 9692 -- -- --
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)
1.676 1.76 87.3 0.224 0.224 3.3 5.4 1256

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 1.676 41.06 -- 0.0 -- 9692 550 99.5 -- 0.1688 0.167 0.1977 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 1.676 1.719 -- 32 609 0.219 0.259 -- 93.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.104
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 12.666
r_mcbond_it 0.758
r_bond_refined_d 0.011
r_scbond_it 1.976
r_mcangle_it 1.392
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 2.83
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 34.151
r_scangle_it 3.194
r_chiral_restr 0.085
r_mcbond_other 0.154
r_angle_other_deg 0.872
r_bond_other_d 0.001
r_angle_refined_deg 1.176
r_dihedral_angle_1_deg 6.307
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 806
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 100

Software

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