X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 291.5
Details PEG 6K, MgSO4, cacodylic acid, benzamidine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.5K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.42 α = 90
b = 82.08 β = 90
c = 118.87 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU -- 2004-01-15
Diffraction Radiation
Monochromator Protocol
Ni Filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
2.3 25 99.9 0.097 -- -- 9.0 35678 35653 -- -- 43.0
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)
2.3 2.38 99.4 0.67 -- 2.74 -- 3465

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 2.3 25.0 -- 0.0 35591 33839 1784 99.83 -- 0.197 0.194 0.255 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 2.299 2.358 -- 118 2436 0.241 0.321 0.014 99.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.104
Anisotropic B[1][1] -0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.69
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 1.29
c_improper_angle_d 4.8
c_dihedral_angle_d 24.9
c_angle_deg 3.0
c_angle_d 0.082
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.18
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.25
Luzzati Sigma A (R-Free Set) 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4876
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 277

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.601 data extraction
REFMAC5 refinement
MOLREP molecular replacement
HKL data processing