X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 20% PEG 6000, 0.01M ZnCl2, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.19 α = 72.39
b = 62.42 β = 74.57
c = 66.05 γ = 73.63
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR MAR scanner 345 mm plate -- 2011-09-15
Diffraction Radiation
Monochromator Protocol
CONFOCAL MAXFLUX MIRRORS 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
2.63 50 97.0 0.088 -- -- 4.7 14526 14526 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)
2.63 2.68 94.3 0.373 -- -- 4.4 718

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 2.63 48.68 -- 0.0 14469 14469 732 96.32 -- 0.2369 0.2349 0.2751 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 2.628 2.696 -- 56 963 0.404 0.455 -- 91.23
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 65.7281
Anisotropic B[1][1] 0.1
Anisotropic B[1][2] -1.22
Anisotropic B[1][3] 0.59
Anisotropic B[2][2] 4.33
Anisotropic B[2][3] 1.29
Anisotropic B[3][3] -4.85
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.988
r_scbond_it 1.25
r_mcangle_it 0.977
r_mcbond_other 0.081
r_bond_refined_d 0.004
r_bond_other_d 0.001
r_angle_refined_deg 0.921
r_angle_other_deg 0.881
r_dihedral_angle_1_deg 3.746
r_dihedral_angle_2_deg 25.746
r_dihedral_angle_3_deg 9.963
r_dihedral_angle_4_deg 7.481
r_chiral_restr 0.04
r_gen_planes_refined 0.002
r_gen_planes_other 0.001
r_mcbond_it 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1512
Nucleic Acid Atoms 1628
Heterogen Atoms 14
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.1.4 molecular replacement
SCALEPACK data reduction
DENZO data collection