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_long_range_B_other 5.948
r_long_range_B_refined 5.949
r_scangle_other 3.271
r_scbond_other 1.892
r_scbond_it 1.892
r_mcangle_other 3.917
r_mcangle_it 3.918
r_mcbond_other 2.245
r_mcbond_it 2.246
r_gen_planes_other 0.004
r_gen_planes_refined 0.007
r_chiral_restr 0.076
r_dihedral_angle_4_deg 16.783
r_dihedral_angle_3_deg 19.479
r_dihedral_angle_2_deg 35.633
r_dihedral_angle_1_deg 6.969
r_angle_other_deg 1.146
r_angle_refined_deg 1.502
r_bond_other_d 0.004
r_bond_refined_d 0.011
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

Computing
Computing Package Purpose
MXCube Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0032 refinement
MXCube data collection