X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Details HANGING DROP VAPOR DIFFUSION AT 4C, WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA, 0.06 MM HIN, 10 MM HEPES (PH 7.5), 5 MM CACL2, 13 MM NACL, 2.8% V/V PEG400, AND 1.56 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM HEPES (PH 7.5), 50 MM CACL2, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%., pH 7.50, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.61 α = 90
b = 82 β = 90
c = 43.73 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate -- 1997-09-01
Diffraction Radiation
Monochromator Protocol
-- MOLECULAR REPLACEMENT WITH 1IJW HAVING THE PROPER DNA SUBSTITUTIONS AS THE STARTING MODEL.
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 -- NSLS X25

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
2.24 14 81.27 -- 0.068 -- 15.0 -- 6235 -- 0.0 67.0
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)
2.24 2.34 50.8 -- 0.215 2.1 1.49 --

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 2.24 14.0 -- 0.0 -- 6235 630 81.27 -- 0.2439 0.2439 0.3057 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 2.24 2.34 -- 42 432 0.466 0.4314 -- 50.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC_FIXED_ISOTROPIC
Mean Isotropic B 64.0
Anisotropic B[1][1] 19.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -21.52
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 9.24
c_scbond_it 6.1
c_mcangle_it 6.22
c_mcbond_it 4.09
c_improper_angle_d 1.489
c_bond_d 0.007
c_angle_deg 1.251
c_dihedral_angle_d 19.443
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.47
Luzzati Sigma A (Observed) 0.74
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.73
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 323
Nucleic Acid Atoms 568
Heterogen Atoms 8
Solvent Atoms 13

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
CNS model building