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 (Insunorm R, lot # I 550005), cryoprotectant: mother liquor + 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.83 α = 90
b = 80.83 β = 90
c = 33.16 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- --
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE D03B-MX1 -- LNLS D03B-MX1

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
1.47 40.42 99.3 -- 0.058 -- 6.0 13635 13635 -- -- --
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)
1.471 1.55 100.0 0.275 0.275 2.4 5.7 2005

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 1.471 40.41 -- 0.0 -- 13635 683 99.34 -- 0.1563 0.1529 0.2231 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 1.471 1.509 -- 61 968 0.174 0.249 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.3077
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.09
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.27
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.56
r_chiral_restr 0.292
r_mcbond_other 0.579
r_mcbond_it 1.685
r_scbond_it 3.94
r_scangle_it 5.677
r_bond_refined_d 0.02
r_angle_other_deg 1.136
r_dihedral_angle_3_deg 12.28
r_rigid_bond_restr 1.681
r_dihedral_angle_2_deg 32.049
r_mcangle_it 2.571
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_angle_refined_deg 1.8
r_dihedral_angle_4_deg 4.291
r_bond_other_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 808
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 127

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
Marresearch data collection