X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 38% PEG400, 0.1M Bis-tris, pH7.5, 50mM CaCl2, 60mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.67 α = 90
b = 61.67 β = 90
c = 98.8 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2006-05-19
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A

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
1.75 50 99.3 0.075 -- -- 5.3 42012 42012 -- -- 23.2
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)
1.75 1.81 93.2 0.316 -- 3.7 3.2 3957

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 1.75 29.44 -- -- -- 39901 2072 100.0 -- 0.18748 0.18501 0.23624 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 1.751 1.797 -- 127 2688 0.237 0.326 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 28.704
Anisotropic B[1][1] 0.61
Anisotropic B[1][2] 0.3
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.91
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.304
r_dihedral_angle_1_deg 6.017
r_scbond_it 2.487
r_mcbond_it 1.088
r_angle_refined_deg 1.531
r_symmetry_hbond_refined 0.118
r_dihedral_angle_4_deg 19.194
r_symmetry_vdw_refined 0.272
r_chiral_restr 0.099
r_dihedral_angle_2_deg 34.432
r_gen_planes_refined 0.006
r_nbd_refined 0.213
r_xyhbond_nbd_refined 0.16
r_dihedral_angle_3_deg 14.91
r_mcangle_it 1.783
r_bond_refined_d 0.015
r_scangle_it 3.882
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3062
Nucleic Acid Atoms 0
Heterogen Atoms 51
Solvent Atoms 338

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
AMoRE phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling