X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 100 nL complex (4 mg/mL ARF1) and 100 nL crystallization buffer (10% PEG 20K, Glycine pH 8.5, 7.5% propanediol), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.52 α = 90
b = 105.19 β = 98.14
c = 127.91 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2011-09-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1

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
2.9 35 98.7 0.16 -- -- 2.6 -- 25033 -- -3.0 55.0
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)
2.9 3.06 98.8 0.634 -- 1.7 2.6 3622

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 2.9 33.81 -- -- -- 23815 1203 98.41 -- 0.21626 0.21413 0.25932 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 2.9 2.975 -- 88 1736 0.358 0.394 -- 98.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.427
Anisotropic B[1][1] -2.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.21
Anisotropic B[2][2] 3.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.73
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 19.479
r_angle_other_deg 1.146
r_chiral_restr 0.076
r_scbond_it 1.892
r_bond_other_d 0.004
r_dihedral_angle_1_deg 6.969
r_gen_planes_refined 0.007
r_mcbond_it 2.246
r_bond_refined_d 0.011
r_long_range_B_refined 5.949
r_long_range_B_other 5.948
r_angle_refined_deg 1.502
r_scangle_other 3.271
r_dihedral_angle_4_deg 16.783
r_scbond_other 1.892
r_mcangle_other 3.917
r_mcangle_it 3.918
r_gen_planes_other 0.004
r_mcbond_other 2.245
r_dihedral_angle_2_deg 35.633
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5386
Nucleic Acid Atoms 855
Heterogen Atoms 0
Solvent Atoms 33

Software

Software
Software Name Purpose
MxCuBE data collection
REFMAC refinement version: 5.7.0032
MOSFLM data reduction
SCALA data scaling