X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 290.0
Details 10MM SODIUM PHOSPHATE, 1mM CACL2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.76 α = 90
b = 42.76 β = 90
c = 65.76 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Mirror 2008-04-19
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 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
1.8 42.8 98.4 -- 0.042 -- -- 10374 10374 0.0 0.0 --
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)
1.76 1.8 96.8 -- 0.164 3.0 -- --

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 1.8 35.85 -- -- 10374 10374 522 98.42 -- 0.17291 0.17097 0.21019 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 1.798 1.844 -- 27 761 0.342 0.535 -- 96.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.703
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.46
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.01
r_mcangle_it 2.725
r_angle_refined_deg 1.98
r_dihedral_angle_4_deg 17.208
r_dihedral_angle_3_deg 16.432
r_dihedral_angle_1_deg 6.68
r_mcbond_it 1.393
r_scangle_it 6.37
r_chiral_restr 0.139
r_dihedral_angle_2_deg 33.683
r_bond_refined_d 0.024
r_scbond_it 4.133
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 963
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 95

Software

Software
Software Name Purpose
HKL-2000 data collection
AMoRE phasing
REFMAC refinement version: 5.5.0072
DENZO data reduction
SCALEPACK data scaling