X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 298.0
Details PEG 20K, MnSO4, NaoAc, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.07 α = 90
b = 97.07 β = 90
c = 48.89 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-04-03
CCD ADSC QUANTUM 4 -- 2005-05-15
Diffraction Radiation
Monochromator Protocol
ALS monochromator SINGLE WAVELENGTH
SSRL monochromater MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL1-5 0.9794, 0.9796, 0.9537 SSRL BL1-5
SYNCHROTRON ALS BEAMLINE 8.2.1 0.9791 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
2 18 99.8 0.073 0.073 -- 7.0 -- 15517 2.3 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)
2.0 2.11 99.9 0.224 0.224 2.6 6.5 --

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 2.0 18.0 -- 0.0 -- 15471 771 99.5 0.199 0.199 0.197 0.231 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 2.0 2.052 -- 67 1075 0.199 0.239 -- 99.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.606
Anisotropic B[1][1] -0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.51
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.182
r_dihedral_angle_2_deg 38.387
r_symmetry_vdw_refined 0.249
r_angle_refined_deg 1.071
r_scangle_it 2.94
r_dihedral_angle_3_deg 13.663
r_mcangle_it 1.109
r_nbtor_refined 0.291
r_symmetry_hbond_refined 0.124
r_bond_refined_d 0.009
r_dihedral_angle_4_deg 22.75
r_mcbond_it 0.695
r_gen_planes_refined 0.003
r_dihedral_angle_1_deg 5.219
r_chiral_restr 0.066
r_xyhbond_nbd_refined 0.118
r_scbond_it 1.862
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1514
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 86

Software

Software
Software Name Purpose
SCALA data scaling
SOLVE phasing version: 2.08
RESOLVE phasing version: 2.08
REFMAC refinement
PDB_EXTRACT data extraction version: 1.700
Blu-Ice data collection
CCP4 data scaling version: (SCALA)