X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 10mM Hepes, 20% PEG 4000, 5% iso-propanol, 0.05M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.06 α = 82.62
b = 47.38 β = 80.91
c = 81.46 γ = 65.4
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2006-12-10
CCD ADSC QUANTUM 315 -- 2006-11-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.07158 SPring-8 BL41XU
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A

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
1.7 50 -- 0.062 -- -- 2.2 -- 65343 -- -- --
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)
1.7 1.76 -- 0.267 -- 2.6 -- --

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 1.7 39.16 -- -- -- 62030 3287 94.1 -- 0.16527 0.16314 0.20557 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 1.699 1.743 -- 206 3855 0.228 0.306 -- 79.42
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.863
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_metal_ion_refined 0.215
r_dihedral_angle_2_deg 38.577
r_symmetry_hbond_refined 0.102
r_dihedral_angle_1_deg 5.607
r_gen_planes_refined 0.006
r_bond_refined_d 0.012
r_chiral_restr 0.115
r_xyhbond_nbd_refined 0.129
r_symmetry_vdw_refined 0.166
r_nbtor_refined 0.312
r_angle_refined_deg 1.4
r_dihedral_angle_4_deg 15.733
r_scbond_it 2.378
r_nbd_refined 0.217
r_mcbond_it 0.76
r_mcangle_it 1.372
r_dihedral_angle_3_deg 14.565
r_symmetry_metal_ion_refined 0.135
r_scangle_it 3.849
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5796
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 619

Software

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