X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 1.5M AMMONIUM PHOSPHATE, 0.1M MES BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 162.32 α = 90
b = 58.35 β = 109.61
c = 138.27 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2008-12-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 -- SPRING-8 BL38B1

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
1.99 50 95.1 0.072 -- -- 3.4 -- 79673 -- -- --
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)
1.99 2.06 82.1 0.287 -- -- 3.1 --

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 1.99 28.99 -- 0.0 -- 75684 3985 94.8 -- 0.198 0.196 0.248 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 1.99 2.04 -- 236 4525 0.25 0.335 -- 77.36
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.68
Anisotropic B[1][1] 0.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.13
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.579
r_scbond_it 2.635
r_mcangle_it 1.814
r_mcbond_it 1.146
r_nbd_refined 0.209
r_gen_planes_refined 0.009
r_chiral_restr 0.135
r_dihedral_angle_4_deg 15.891
r_dihedral_angle_3_deg 16.314
r_dihedral_angle_2_deg 36.686
r_dihedral_angle_1_deg 7.033
r_angle_refined_deg 1.845
r_bond_refined_d 0.022
r_nbtor_refined 0.317
r_xyhbond_nbd_refined 0.148
r_symmetry_vdw_refined 0.219
r_symmetry_hbond_refined 0.238
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9201
Nucleic Acid Atoms 0
Heterogen Atoms 158
Solvent Atoms 265

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement