X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details Protein stock solution: 10mg/ml protein in 500mM NaCl, 25mM Tris/HCl, pH 8.5 Emodin stock solution: 10mM in water Protein/emodin mixture: equal volumes of protein and emodin stock solutions were mixed and equillibrated for 30 min prior to crystallization Reservoir: 30% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.6 Crystallization drop: 2 microliters protein/emodin mixture plus 1 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.73 α = 90
b = 45.68 β = 111.8
c = 63.24 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 MARMOSAIC 225 mm CCD -- 2007-02-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9537 EMBL/DESY, Hamburg X12

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
1.95 19.7 99.9 0.112 0.112 -- 4.5 22799 22776 0.0 0.0 25.1
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)
1.95 2.02 100.0 0.626 0.626 2.0 4.5 2247

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 1.95 19.7 0.0 0.0 22776 21615 1161 99.67 0.1877 0.1877 0.18522 0.23346 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 1.953 2.003 -- 80 1554 0.222 0.378 -- 97.32
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic plus TLS refinement
Mean Isotropic B 24.78
Anisotropic B[1][1] -3.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.37
Anisotropic B[2][2] 3.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.14
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.087
r_angle_refined_deg 1.397
r_gen_planes_other 0.001
r_symmetry_vdw_other 0.264
r_mcbond_it 3.833
r_symmetry_hbond_refined 0.192
r_dihedral_angle_3_deg 14.57
r_bond_other_d 0.001
r_dihedral_angle_4_deg 18.86
r_gen_planes_refined 0.006
r_angle_other_deg 0.918
r_mcangle_it 4.315
r_nbtor_other 0.089
r_nbtor_refined 0.19
r_dihedral_angle_1_deg 5.963
r_bond_refined_d 0.013
r_scangle_it 4.748
r_symmetry_vdw_refined 0.136
r_nbd_refined 0.215
r_nbd_other 0.196
r_xyhbond_nbd_refined 0.179
r_dihedral_angle_2_deg 33.282
r_mcbond_other 1.31
r_scbond_it 3.674
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2773
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 300

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling