X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 293.15
Details PEG 6000, ammonium sulfate, tris-HCl, benzamidine, calcium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.28 α = 90
b = 58.57 β = 90
c = 66.14 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
ENRAF-NONIUS ENRAF-NONIUS -- 2000-06-09
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR590 -- -- --

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
1.2 19.9 97.4 0.061 -- -- 10.5 64859 64859 0.0 0.0 11.6
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)
1.2 1.24 77.1 0.429 -- 1.5 2.1 6239

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 1.21 19.9 0.0 0.0 64546 64546 3273 99.4 0.161 0.161 0.16 0.178 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 1.21 1.25 6239 343 -- 0.253 0.276 -- 97.5
X Ray Diffraction 1.25 1.3 6364 333 -- 0.235 0.254 -- 99.1
X Ray Diffraction 1.3 1.36 6398 322 -- 0.213 0.202 -- 99.6
X Ray Diffraction 1.36 1.43 6406 339 -- 0.185 0.195 -- 99.7
X Ray Diffraction 1.43 1.52 6413 299 -- 0.161 0.171 -- 99.6
X Ray Diffraction 1.52 1.64 6441 351 -- 0.147 0.156 -- 99.5
X Ray Diffraction 1.64 1.81 6434 305 -- 0.141 0.161 -- 99.4
X Ray Diffraction 1.81 2.07 6497 323 -- 0.144 0.172 -- 99.8
X Ray Diffraction 2.07 2.61 6565 350 -- 0.14 0.164 -- 99.8
X Ray Diffraction 2.61 19.9 6789 308 -- 0.146 0.16 -- 99.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 9.5
Anisotropic B[1][1] -8.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.674
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.138
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 1.453
c_scangle_it 1.908
c_mcbond_it 0.753
c_mcangle_it 1.077
c_improper_angle_deg 1.023
c_dihedral_angle_deg 25.877
c_bond_d 0.00839
c_angle_deg 1.574
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.12
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.13
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1629
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 385

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection