X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 298.0
Details microseeding in 100 mM sodium acetate (pH 4.6), 100 mM ammonium acetate, 24% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 33.94 α = 90
b = 42.24 β = 90
c = 63.67 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 NOIR-1 -- 2006-07-15
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.07 ALS 4.2.2

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 42.24 96.2 -- 0.048 -- 6.13 -- 48392 -- -- 7.9
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)
1.0 1.04 67.9 -- 0.479 1.8 2.8 3351

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 1.0 35.2 -- -- -- 45895 2428 96.22 0.13465 0.13465 0.13346 0.1582 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 1.0 1.026 2354 135 2219 0.38 0.41 -- 64.25
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.51
Anisotropic B[1][1] -0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_xyhbond_nbd_refined 0.161
r_scangle_it 6.804
r_nbd_other 0.195
r_chiral_restr 0.146
r_symmetry_vdw_refined 0.231
r_dihedral_angle_3_deg 11.38
r_dihedral_angle_1_deg 5.745
r_nbtor_refined 0.18
r_angle_refined_deg 2.192
r_mcbond_other 0.965
r_rigid_bond_restr 2.307
r_scbond_it 4.973
r_sphericity_free 15.363
r_dihedral_angle_2_deg 38.081
r_mcbond_it 2.711
r_mcangle_it 3.374
r_gen_planes_refined 0.01
r_nbtor_other 0.098
r_angle_other_deg 1.007
r_nbd_refined 0.223
r_dihedral_angle_4_deg 28.105
r_symmetry_hbond_refined 0.178
r_bond_refined_d 0.034
r_symmetry_vdw_other 0.21
r_sphericity_bonded 5.443
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1684
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 175

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
JBluIce-EPICS data collection
d*TREK data reduction
d*TREK data scaling
MOLREP phasing