X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 2 uL mother liquor (0.1 M MES, pH 6.5, 1.6 M magnesium sulfate heptahydrate) + 2 uL protein (aspart insulin, 100 U/mL), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.29 α = 90
b = 78.29 β = 90
c = 36.91 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2011-10-17
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
2.5 39.15 89.3 -- 0.076 -- 1.7 2607 2607 -- -- --
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)
2.502 2.64 92.5 0.47 0.47 1.0 1.6 396

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 2.502 39.145 -- 0.0 -- 2602 232 89.08 -- 0.1578 0.1525 0.2023 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 2.502 2.565 -- 17 179 0.136 0.283 -- 90.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.5013
Anisotropic B[1][1] -8.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 16.67
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.018
r_dihedral_angle_4_deg 27.847
r_angle_other_deg 1.125
r_dihedral_angle_2_deg 42.211
r_bond_other_d 0.002
r_chiral_restr 0.11
r_gen_planes_refined 0.007
r_dihedral_angle_1_deg 7.252
r_gen_planes_other 0.001
r_angle_refined_deg 1.954
r_dihedral_angle_3_deg 20.623
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 803
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 2

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.20
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
MAR345 data collection