X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.3
Temperature 295.0
Details 25% PEG-MME 5000, 0.1 M OAc, pH 5.3, VAPOR DIFFUSION, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.79 α = 92.51
b = 43.33 β = 94.96
c = 58.46 γ = 90.55
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU -- -- --

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
2.5 42.64 96.0 0.071 -- -- 1.9 -- 13814 -- -- --
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)
2.5 2.59 89.8 0.473 -- -- 1.8 1281

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 2.503 42.64 -- 0.0 -- 13800 695 95.77 -- 0.211 0.208 0.277 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 2.503 2.568 -- 52 862 0.289 0.433 -- 87.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.705
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.17
Anisotropic B[1][3] 0.14
Anisotropic B[2][2] 0.35
Anisotropic B[2][3] 0.07
Anisotropic B[3][3] -0.32
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_nbtor_refined 0.181
r_symmetry_hbond_refined 0.248
r_mcbond_other 0.109
r_symmetry_vdw_refined 0.142
r_gen_planes_refined 0.005
r_angle_refined_deg 1.573
r_gen_planes_other 0.001
r_nbd_other 0.194
r_xyhbond_nbd_refined 0.168
r_dihedral_angle_2_deg 32.969
r_nbd_refined 0.208
r_scbond_it 1.436
r_dihedral_angle_3_deg 16.408
r_nbtor_other 0.091
r_angle_other_deg 0.843
r_dihedral_angle_1_deg 6.974
r_scangle_it 2.258
r_dihedral_angle_4_deg 14.995
r_symmetry_vdw_other 0.242
r_mcangle_it 1.01
r_mcbond_it 0.548
r_bond_refined_d 0.016
r_xyhbond_nbd_other 0.033
r_chiral_restr 0.083
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3417
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 63

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement version: 5.2.0007
PDB_EXTRACT data extraction version: 3.000
ADSC data collection version: Quantum
HKL-2000 data reduction