X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 278.0
Details Protein solution: 10mM MOPS buffer pH 7.0, 50 mM NaCl, 3mM MnCl2, 0.2 mM ATP. Well solution: 0.5 M (NH4)2SO4, 0.1 M HEPES, 10 % MPD, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.52 α = 90
b = 80.55 β = 90
c = 97.62 γ = 90
Symmetry
Space Group P 21 21 21

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
SYNCHROTRON ALS BEAMLINE 8.2.1 1.00000 ALS 8.2.1

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
1.6 50 99.49 -- -- -- -- -- 60216 -- 2.0 --
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)
1.6 1.642 96.54 -- -- -- -- 4022

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 1.6 50.0 -- 0.0 -- 60216 3040 99.49 -- 0.179 0.177 0.205 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 1.6 1.642 -- 224 4022 0.253 0.285 -- 96.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.314
Anisotropic B[1][1] -0.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.32
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.078
r_angle_other_deg 0.916
r_nbd_refined 0.228
r_mcbond_it 0.652
r_symmetry_hbond_refined 0.103
r_scbond_it 1.249
r_scangle_it 1.786
r_dihedral_angle_3_deg 11.761
r_rigid_bond_restr 0.63
r_dihedral_angle_4_deg 15.748
r_bond_other_d 0.001
r_chiral_restr 0.065
r_gen_planes_other 0.001
r_nbtor_refined 0.183
r_symmetry_vdw_other 0.175
r_mcbond_other 0.164
r_xyhbond_nbd_refined 0.113
r_dihedral_angle_2_deg 33.955
r_mcangle_it 0.733
r_dihedral_angle_1_deg 5.073
r_nbd_other 0.193
r_bond_refined_d 0.007
r_angle_refined_deg 1.128
r_sphericity_free 2.632
r_sphericity_bonded 0.805
r_gen_planes_refined 0.003
r_symmetry_vdw_refined 0.099
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2869
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 394

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.006
HKL-2000 data collection