X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 293.0
Details PEG6000, BisTrisHCl, mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.18 α = 103.1
b = 68.85 β = 98.79
c = 58.52 γ = 78.98
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ double crystal monochromator and bent-cylinder mirror 2000-01-01
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL40B2 0.7000 SPRING-8 BL40B2

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
2.1 30 89.4 0.032 -- -- 2.39 57103 51056 0.0 0.5 20.12
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)
2.1 2.18 70.9 0.155 -- 2.63 1.63 5699

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 2.1 30.0 -- 0.0 57103 51056 2549 89.4 0.2 0.2 0.198 0.24 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 2.1 2.18 4038 182 3749 0.2474 0.2996 -- 70.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 25.3
Anisotropic B[1][1] 0.493
Anisotropic B[1][2] -4.034
Anisotropic B[1][3] 5.198
Anisotropic B[2][2] 2.688
Anisotropic B[2][3] 4.241
Anisotropic B[3][3] -3.181
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.56
c_scbond_it 1.76
c_mcangle_it 2.41
c_mcbond_it 1.46
c_improper_angle_d 0.72
c_dihedral_angle_d 23.3
c_angle_deg 1.17
c_bond_d 0.0065
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.175
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6755
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 205

Software

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