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_rigid_bond_restr 1.681
r_scangle_it 5.677
r_scbond_it 3.94
r_mcangle_it 2.571
r_mcbond_other 0.579
r_bond_refined_d 0.02
r_bond_other_d 0.002
r_angle_refined_deg 1.8
r_angle_other_deg 1.136
r_dihedral_angle_1_deg 6.56
r_dihedral_angle_2_deg 32.049
r_dihedral_angle_3_deg 12.28
r_dihedral_angle_4_deg 4.291
r_chiral_restr 0.292
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_mcbond_it 1.685
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

Computing
Computing Package Purpose
Marresearch 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