X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.35 α = 90
b = 40.35 β = 90
c = 118 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2003-02-07
Diffraction Radiation
Monochromator Protocol
Si(111) double monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.650 SPRING-8 BL41XU

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
1.2 35 94.5 -- 0.037 -- 8.3 33512 31902 0.0 0.0 14.3
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)
1.2 1.24 82.4 -- 0.368 3.4 5.6 3170

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 1.2 34.92 -- 0.0 31742 31742 1699 -- 0.16658 0.16658 0.16523 0.19113 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 1.202 1.233 -- 136 2150 0.261 0.272 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.293
Anisotropic B[1][1] 0.49
Anisotropic B[1][2] 0.25
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.74
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.835
r_nbtor_other 0.1
r_nbd_other 0.291
r_nbd_refined 0.287
r_gen_planes_other 0.008
r_gen_planes_refined 0.008
r_chiral_restr 0.098
r_dihedral_angle_1_deg 5.941
r_angle_other_deg 0.806
r_angle_refined_deg 1.44
r_bond_other_d 0.0
r_bond_refined_d 0.011
r_xyhbond_nbd_refined 0.243
r_symmetry_vdw_refined 0.156
r_symmetry_vdw_other 0.212
r_symmetry_hbond_refined 0.25
r_mcbond_it 1.187
r_mcangle_it 1.853
r_scbond_it 2.141
r_scangle_it 3.243
r_rigid_bond_restr 1.15
r_sphericity_free 2.973
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 949
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 180

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement