X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 291.0
Details SODIUM FORMATE, SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 125.73 α = 90
b = 125.73 β = 90
c = 74.63 γ = 120
Symmetry
Space Group P 64

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 BENT CYLINDRICAL SI-MIRROR (RH COATING) 2000-06-14
Diffraction Radiation
Monochromator Protocol
SI(111) DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 1.006 APS 14-BM-D

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
2.5 20 96.4 0.077 -- -- 50.8 21919 21919 0.0 0.0 74.6
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)
2.52 2.56 76.2 0.599 -- 1.6 6.0 --

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 2.5 20.0 0.0 0.0 21919 20796 1123 96.4 -- -- 0.2466 0.2547 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 2.522 2.637 -- 115 -- 0.39 0.474 -- 79.3
X Ray Diffraction 2.637 2.764 -- 123 -- 0.283 0.326 -- 91.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC ATOMIC TEMPERATURE FACTORS
Mean Isotropic B -0.01087
Anisotropic B[1][1] 1.214
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.267
Anisotropic B[2][2] 0.268
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.095
RMS Deviations
Key Refinement Restraint Deviation
p_transverse_tor 21.5
p_staggered_tor 19.5
p_planar_tor 3.7
p_xhyhbond_nbd 0.178
p_multtor_nbd 0.267
p_bond_d 0.019
p_angle_d 0.055
p_planar_d 0.05
p_mcbond_it 2.487
p_mcangle_it 4.021
p_scbond_it 3.469
p_scangle_it 5.213
p_plane_restr 0.0251
p_chiral_restr 0.204
p_singtor_nbd 0.215
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27134
Luzzati ESD (R-Free Set) 0.21384
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2122
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 47

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
AMORE model building
SCALEPACK data reduction
DENZO data collection