X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 293.0
Details 40% PEG2000, 100mM sodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.42 α = 90
b = 40.42 β = 90
c = 118.13 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 2004-03-26
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
1.34 20.09 99.8 0.053 -- -- 11.1 -- 23170 -- -- --
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)
1.34 1.39 99.8 0.303 -- 9.09 11.0 --

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 1.34 20.0 -- -- -- 23170 1244 99.91 -- 0.15397 0.15209 0.18915 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 1.34 -- -- -- 1706 -- -- -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.989
Anisotropic B[1][1] 0.53
Anisotropic B[1][2] 0.27
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.8
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 4.264
r_sphericity_free 5.36
r_rigid_bond_restr 2.094
r_scangle_it 3.615
r_scbond_it 2.857
r_mcangle_it 2.289
r_mcbond_it 1.596
r_symmetry_hbond_refined 0.164
r_bond_refined_d 0.012
r_angle_refined_deg 1.487
r_dihedral_angle_1_deg 6.074
r_dihedral_angle_2_deg 36.474
r_dihedral_angle_3_deg 15.769
r_dihedral_angle_4_deg 12.98
r_chiral_restr 0.102
r_gen_planes_refined 0.008
r_nbd_refined 0.257
r_nbtor_refined 0.316
r_xyhbond_nbd_refined 0.185
r_symmetry_vdw_refined 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 968
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 210

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