X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details HEPES, ammonium sulfate, glycerol, PEG 400, benzamidine, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.44 α = 90
b = 84.51 β = 90
c = 84.84 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-12-08
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.05 ALS 5.0.2

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 35 99.9 0.062 -- -- 4.044 33624 33624 0.0 0.0 33.6
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)
2.0 2.07 99.7 0.422 -- 3.4 3.77 3318

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 2.0 35.0 0.0 0.2 33404 33404 698 99.9 0.212 0.212 0.204 0.227 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 2.0 2.07 3259 59 3230 0.313 0.34 0.044 99.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.6
Anisotropic B[1][1] 5.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.25
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 5.9
x_scbond_it 4.07
x_mcangle_it 4.47
x_mcbond_it 2.97
x_improper_angle_d 1.1
x_dihedral_angle_d 24.2
x_angle_deg 1.5
x_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2415
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 198

Software

Computing
Computing Package Purpose
ADSC (QUANTUM) Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 98.1 Structure Refinement
Software
Software Name Purpose
X-PLOR(ONLINE) version: 98.1 refinement
AMoRE model building
SCALEPACK data reduction
ADSC version: Quantum data collection