X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.57
Temperature 277.0
Details NANODROP, 23.4% PEG 4000, 15.0% Glycerol, 0.17M Ammonium acetate, 0.1M Citric acid pH 5.57, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.17 α = 90
b = 71.17 β = 90
c = 325.5 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2007-06-03
Diffraction Radiation
Monochromator Protocol
Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97903, 0.97920 SSRL BL9-2

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
1.65 29.76 100.0 0.147 0.147 -- 10.6 -- 60310 -- -- 17.94
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)
1.65 1.69 100.0 0.012 1.24 2.0 10.8 4353

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
MAD 1.65 29.761 -- 0.0 -- 60156 3039 99.97 -- 0.154 0.152 0.18 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 1.65 1.693 4345 241 4104 0.225 0.289 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.037
Anisotropic B[1][1] 0.51
Anisotropic B[1][2] 0.25
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.76
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_dihedral_angle_2_deg 32.898
r_gen_planes_refined 0.007
r_symmetry_vdw_other 0.28
r_symmetry_hbond_refined 0.195
r_nbtor_other 0.085
r_scangle_it 7.126
r_mcangle_it 2.477
r_dihedral_angle_4_deg 15.408
r_gen_planes_other 0.002
r_xyhbond_nbd_other 0.059
r_mcbond_it 1.873
r_nbd_refined 0.235
r_nbd_other 0.19
r_mcbond_other 0.511
r_angle_other_deg 1.054
r_angle_refined_deg 1.764
r_xyhbond_nbd_refined 0.194
r_bond_refined_d 0.017
r_scbond_it 4.947
r_chiral_restr 0.1
r_symmetry_vdw_refined 0.353
r_dihedral_angle_1_deg 5.428
r_nbtor_refined 0.182
r_dihedral_angle_3_deg 11.702
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3025
Nucleic Acid Atoms 0
Heterogen Atoms 91
Solvent Atoms 410

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
SCALA data scaling
PDB_EXTRACT data extraction version: 3.00
MAR345 data collection version: CCD
MOSFLM data reduction
SHELXD phasing
SOLVE phasing