X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 5.9
Temperature 295.0
Details Na Citrate 0.72M, Acetate 0.1M, pH 5.9, microbatch, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 131.23 α = 90
b = 131.23 β = 90
c = 110.61 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH mirrors 2002-12-10
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.980 SPring-8 BL44B2

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
2.85 40 99.95 0.068 -- -- 7.69 66615 15761 0.0 0.0 70.8
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)
2.85 2.98 86.2 0.451 -- 5.7 5.0 1684

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 2.85 40.0 0.0 0.0 16595 14983 778 95.0 -- -- 0.2035 0.267 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 2.85 2.98 1781 97 -- 0.308 0.309 0.031 86.2
X Ray Diffraction 2.98 3.14 1976 98 -- 0.27 0.298 0.03 94.1
X Ray Diffraction 3.14 3.34 1841 91 -- 0.275 0.4 0.042 89.9
X Ray Diffraction 3.34 3.59 1978 91 -- 0.232 0.321 0.034 96.4
X Ray Diffraction 3.59 4.53 2067 95 -- 0.181 0.215 0.022 98.1
X Ray Diffraction 4.53 5.7 2031 97 -- 0.154 0.226 0.023 98.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.89
Anisotropic B[1][1] -7.06
Anisotropic B[1][2] 0.75
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 14.13
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 21.1
c_improper_angle_d 0.96
c_angle_deg 1.2
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.4
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.41
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1907
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 72

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
CNS refinement version: 1.1
HKL-2000 data reduction
CNS phasing version: 1.1