X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 10 mM calcium chloride, 0.1 M HEPES, 1.8 M ammonium sulfate, 0.02% sodium azide; 20% ethylene glycol added upon harvesting and prior to freezing, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.73 α = 90
b = 81.91 β = 90
c = 124.26 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) 2002-08-20
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
1.6 20 99.9 0.05 -- -- 10.3 50718 50681 0.0 -3.0 22.4
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)
1.6 1.66 99.3 0.241 -- 4.63 4.5 4959

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 1.62 20.0 -3.0 0.0 48724 48719 3953 100.0 0.2149 0.2149 0.2138 0.2273 RANDOM, SAME TEST SET AS FOR PDB ID 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 1.62 1.72 8008 667 7341 0.251 0.274 -- 99.93
X Ray Diffraction 1.72 1.85 8057 648 -- 0.255 0.293 -- 100.0
X Ray Diffraction 1.85 2.04 8042 625 -- 0.238 0.266 -- 100.0
X Ray Diffraction 2.04 2.34 8102 654 -- 0.227 0.244 -- 100.0
X Ray Diffraction 2.34 2.94 8126 657 -- 0.215 0.241 -- 100.0
X Ray Diffraction 2.94 20.0 8384 702 -- 0.184 0.182 -- 99.99
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 17.3
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.167
c_scbond_it 1.521
c_mcangle_it 1.493
c_mcbond_it 0.979
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) 0.21
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2071
Nucleic Acid Atoms 0
Heterogen Atoms 67
Solvent Atoms 260

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