X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6
Temperature 293.0
Details 40% PEG2000, 100mM sodium citrate, pH 6.0, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.02 α = 90
b = 37.02 β = 90
c = 129.62 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 ADSC QUANTUM 4 bending-magnet 2004-01-01
Diffraction Radiation
Monochromator Protocol
fixed-exit double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL40B2 1.000 SPRING-8 BL40B2

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
1.42 25.74 99.9 0.07 -- -- 11.1 -- 18879 -- -- --

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 1.42 20.0 -- -- -- 17895 971 99.95 -- 0.1418 0.1406 0.16346 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 1.42 -- -- -- 1285 -- -- -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.247
Anisotropic B[1][1] 0.22
Anisotropic B[1][2] 0.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.33
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 3.235
r_sphericity_free 5.017
r_rigid_bond_restr 1.537
r_scangle_it 4.012
r_scbond_it 2.811
r_mcangle_it 2.082
r_mcbond_it 1.51
r_symmetry_hbond_refined 0.163
r_bond_refined_d 0.013
r_angle_refined_deg 1.494
r_dihedral_angle_1_deg 5.899
r_dihedral_angle_2_deg 38.164
r_dihedral_angle_3_deg 12.321
r_dihedral_angle_4_deg 14.554
r_chiral_restr 0.105
r_gen_planes_refined 0.009
r_nbd_refined 0.248
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.181
r_symmetry_vdw_refined 0.189
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 974
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 207

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement