X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 10 mM calcium chloride, 0.1 M HEPES, 2.0 M ammonium sulfate, 0.02% sodium azide; 20% ethylene glycol added upon harvesting and prior to freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.59 α = 90
b = 81.74 β = 90
c = 123.6 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NONIUS KAPPA CCD2000 OSMIC CONFOCAL MAX-FLUX (GREEN) 2002-08-04
Diffraction Radiation
Monochromator Protocol
OSMIC CONFOCAL MAX-FLUX (GREEN) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR591 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
1.65 20 99.7 0.046 -- -- 10.0 45596 45459 0.0 -3.0 25.7
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)
1.65 1.71 97.1 0.232 -- 5.6 4.0 4357

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 1.65 20.0 -3.0 0.0 45740 45459 3671 99.4 0.2078 0.2078 0.2068 0.2195 RANDOM; SAME SET AS FOR PDB IDS 2FI3, 2FI4 AND 2FI5
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 1.65 1.75 7239 582 6657 0.253 0.287 -- 96.28
X Ray Diffraction 1.75 1.89 7552 601 -- 0.232 0.258 -- 100.0
X Ray Diffraction 1.89 2.08 7571 586 -- 0.217 0.229 -- 100.0
X Ray Diffraction 2.08 2.38 7569 632 -- 0.219 0.236 -- 100.0
X Ray Diffraction 2.38 3.0 7654 615 -- 0.209 0.227 -- 99.98
X Ray Diffraction 3.0 20.0 7874 655 -- 0.185 0.19 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 18.7
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.176
c_scbond_it 1.523
c_mcangle_it 1.518
c_mcbond_it 1.001
c_improper_angle_d 0.0
c_bond_d 0.005
c_angle_deg 1.3
c_dihedral_angle_d 25.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2076
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 238

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS model building
SCALEPACK data reduction
HKL-2000 data collection