X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.5
Details PROTEIN WAS CRYSTALLIZED FROM: 75 MM NAAC PH4.5, 20 MM MGCL2 AND 23% MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.66 α = 90
b = 39.66 β = 90
c = 47.47 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU MIRRORS 1998-04-15
Diffraction Radiation
Monochromator Protocol
NI FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 -- -- --

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
1.8 20 95.3 0.036 -- -- 6.7 -- 4072 -- -- 27.8
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)
1.8 1.91 92.4 0.295 -- 4.3 4.5 --

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 1.8 20.0 -- 0.0 -- 4072 378 95.3 -- 0.211 0.211 0.236 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 1.8 1.91 -- 63 566 0.314 0.353 0.044 92.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.0
Anisotropic B[1][1] 4.87
Anisotropic B[1][2] 2.63
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.87
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.74
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.3
c_mcangle_it 1.92
c_scbond_it 2.79
c_angle_deg 1.2
c_mcbond_it 1.33
c_bond_d 0.011
c_improper_angle_d 0.84
c_dihedral_angle_d 14.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 267
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 47

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.4
DENZO data reduction
SCALEPACK data scaling