X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 12-25% MPD, 0.1M MES buffer pH 6.0, 5mm Caffeine, 30mM GlcNac, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 124.4 α = 90
b = 124.4 β = 90
c = 123.61 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 210 -- 2005-08-25
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID

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
1.8 50 96.8 0.087 -- -- 3.2 197105 190798 -- -3.0 20.7
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)
1.8 1.86 95.5 0.488 -- 1.5 2.6 18805

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 1.8 19.66 -- -- 190798 186135 5803 96.86 -- 0.17468 0.17394 0.19782 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 1.8 1.846 -- 436 13498 0.252 0.271 -- 95.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.015
Anisotropic B[1][1] -0.21
Anisotropic B[1][2] -0.1
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.31
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.003
r_mcangle_it 0.903
r_dihedral_angle_4_deg 14.066
r_bond_other_d 0.001
r_nbd_other 0.179
r_mcbond_other 0.099
r_dihedral_angle_2_deg 34.99
r_chiral_restr 0.061
r_symmetry_vdw_other 0.254
r_bond_refined_d 0.007
r_symmetry_hbond_refined 0.139
r_nbd_refined 0.204
r_nbtor_refined 0.178
r_scangle_it 1.967
r_nbtor_other 0.081
r_scbond_it 1.295
r_dihedral_angle_3_deg 11.917
r_mcbond_it 0.57
r_symmetry_vdw_refined 0.177
r_angle_other_deg 0.842
r_angle_refined_deg 1.113
r_xyhbond_nbd_refined 0.117
r_dihedral_angle_1_deg 5.469
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13003
Nucleic Acid Atoms 0
Heterogen Atoms 224
Solvent Atoms 1353

Software

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