X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 293.0
Details 24% PEG 5000 MME, 6% (v/v) glycerol, 0.4 M NaCl, 0.16 M (NH4)2SO4, 0.08 M Na Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.08 α = 90
b = 106.08 β = 90
c = 70.35 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2005-11-10
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID

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
1.3 20 99.8 -- 0.057 -- 6.9 98312 98154 -3.0 -3.0 15.7
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)
1.3 1.35 100.0 -- 0.444 -- 6.4 9705

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
SAD 1.3 20.0 -- 0.0 96876 96876 4829 98.48 0.167 0.167 0.166 0.182 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 1.301 1.335 7243 354 6793 0.205 0.21 -- 99.72
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic + TLS
Mean Isotropic B 15.626
Anisotropic B[1][1] 0.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.53
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.007
r_dihedral_angle_2_deg 31.849
r_nbd_other 0.192
r_dihedral_angle_4_deg 19.358
r_xyhbond_nbd_refined 0.194
r_nbtor_other 0.082
r_symmetry_vdw_other 0.249
r_mcbond_other 0.214
r_bond_other_d 0.001
r_scangle_it 2.582
r_angle_refined_deg 1.456
r_chiral_restr 0.095
r_bond_refined_d 0.012
r_angle_other_deg 0.827
r_nbtor_refined 0.184
r_dihedral_angle_3_deg 11.934
r_nbd_refined 0.217
r_symmetry_vdw_refined 0.239
r_mcangle_it 1.251
r_dihedral_angle_1_deg 6.161
r_gen_planes_other 0.001
r_symmetry_hbond_refined 0.214
r_mcbond_it 0.738
r_scbond_it 1.775
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2773
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 364

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.10
RESOLVE phasing version: 2.10
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.000
HKL-2000 data collection