X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 3.5
Temperature 277.0
Details 60% (v/v) MPD, Ac2Cu 1 mM, Hepes 15 mM pH 7.0, Counter-diffusion, temperature 277K, pH 3.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.03 α = 90
b = 103.03 β = 90
c = 40.28 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER SMART 6000 MONTEL OPTICS 2006-04-12
Diffraction Radiation
Monochromator Protocol
NI FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE OTHER -- -- --

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
2.7 40.28 99.6 -- 0.0366 -- 11.81 -- 6875 -- -- 58.51
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)
2.7 2.8 98.9 -- 0.3791 3.19 5.8 --

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 2.7 40.28 -- -- -- 6852 324 99.4 -- 0.21 0.206 0.292 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 2.7 2.77 -- 26 463 0.345 0.54 -- 98.39
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.48
Anisotropic B[1][1] -4.304
Anisotropic B[1][2] -2.152
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.304
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.456
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.318
r_symmetry_vdw_refined 0.197
r_xyhbond_nbd_refined 0.199
r_scbond_it 1.251
r_mcangle_it 0.843
r_dihedral_angle_4_deg 19.281
r_dihedral_angle_3_deg 17.876
r_scangle_it 2.095
r_angle_refined_deg 1.619
r_dihedral_angle_2_deg 34.735
r_nbd_refined 0.241
r_symmetry_hbond_refined 0.165
r_mcbond_it 0.474
r_chiral_restr 0.097
r_dihedral_angle_1_deg 6.702
r_bond_refined_d 0.019
r_gen_planes_refined 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1625
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 61

Software

Software
Software Name Purpose
SAINT data scaling
MOLREP phasing
REFMAC refinement version: refmac_5.2.0019
PDB_EXTRACT data extraction version: 1.700
PROTEUM PLUS data reduction version: 2
SADABS data scaling
XPREP data reduction
Coot model building
MolProbity model building