X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 10mM sodium phosphate buffer (Na2HPO4/NaH2PO4), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.58 α = 90
b = 116.58 β = 90
c = 45.91 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2005-10-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1

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
2.1 119.52 99.9 -- -- -- -- -- 36572 -- -3.0 --
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)
2.1 2.18 100.0 -- -- -- -- --

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 2.1 50.0 -- 0.0 -- 34722 1828 99.62 -- 0.16812 0.16654 0.19799 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 2.096 2.15 -- 127 2449 0.227 0.291 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.456
Anisotropic B[1][1] 0.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.09
RMS Deviations
Key Refinement Restraint Deviation
r_metal_ion_refined 0.17
r_mcbond_it 1.33
r_dihedral_angle_1_deg 7.518
r_gen_planes_other 0.004
r_symmetry_vdw_refined 0.285
r_xyhbond_nbd_refined 0.218
r_bond_refined_d 0.026
r_nbd_other 0.268
r_symmetry_hbond_refined 0.168
r_nbd_refined 0.196
r_scbond_it 3.237
r_symmetry_vdw_other 0.332
r_bond_other_d 0.002
r_gen_planes_refined 0.011
r_angle_other_deg 0.944
r_chiral_restr 0.148
r_scangle_it 4.705
r_mcangle_it 2.285
r_nbtor_other 0.096
r_angle_refined_deg 1.985
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2492
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 339

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
HKL-2000 data reduction
SCALEPACK data scaling
MOLREP phasing