X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 20% PEG 3350, 0.2M Sodium sulfate, 10mM Trimethyllead acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 20% PEG 3350, 0.2M Sodium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.93 α = 90
b = 56.93 β = 90
c = 242.54 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2011-09-15
IMAGE PLATE MAR scanner 345 mm plate -- 2011-09-06
Diffraction Radiation
Monochromator Protocol
OSMIC VARIMAX SINGLE WAVELENGTH
OSMIC VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
2.64 99 98.5 0.091 -- -- 2.5 7517 7517 0.0 0.0 --
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)
2.64 2.68 95.0 0.188 -- -- 1.8 344

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
SIRAS 2.64 48.31 -- 0.0 7467 7467 344 99.04 -- 0.2529 0.2523 0.2643 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 2.64 2.709 -- 22 508 0.422 0.42 -- 99.07
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 96.517
Anisotropic B[1][1] 5.31
Anisotropic B[1][2] 2.66
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.97
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 10.185
r_scbond_it 8.122
r_mcangle_it 3.819
r_mcbond_other 0.569
r_bond_refined_d 0.016
r_bond_other_d 0.002
r_angle_refined_deg 2.318
r_angle_other_deg 1.125
r_dihedral_angle_1_deg 5.45
r_dihedral_angle_2_deg 29.747
r_dihedral_angle_3_deg 16.056
r_dihedral_angle_4_deg 14.995
r_chiral_restr 0.083
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_mcbond_it 2.263
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 449
Nucleic Acid Atoms 406
Heterogen Atoms 2
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
RESOLVE version: 2.15 density modification
SOLVE phasing
SCALEPACK data reduction
DENZO data collection