X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 4.6
Temperature 277.0
Details 30.0% MPD, 0.2M NaCl, 0.1M Acetate, pH 4.6 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.15 α = 90
b = 91.15 β = 90
c = 64.77 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-09-09
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SI(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 1.000, 0.9796 ALS 8.2.2

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
1.9 30 99.9 0.096 -- -- 5.3 -- 24794 -- -- --
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)
1.9 1.95 100.0 0.096 -- 1.7 5.4 --

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 1.9 30.0 -- -- -- 23470 1260 99.7 0.168 0.16834 0.166 0.206 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 1.9 1.949 -- 96 1666 0.253 0.326 -- 99.66
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.781
Anisotropic B[1][1] 0.22
Anisotropic B[1][2] 0.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.32
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.017
r_dihedral_angle_2_deg 32.273
r_symmetry_hbond_refined 0.165
r_mcangle_it 3.13
r_dihedral_angle_3_deg 12.624
r_nbtor_other 0.087
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_symmetry_vdw_other 0.271
r_angle_refined_deg 1.542
r_angle_other_deg 0.979
r_metal_ion_refined 0.335
r_dihedral_angle_4_deg 13.382
r_bond_other_d 0.002
r_nbd_refined 0.195
r_mcbond_other 0.517
r_scbond_it 5.351
r_symmetry_vdw_refined 0.153
r_nbd_other 0.196
r_scangle_it 7.478
r_chiral_restr 0.096
r_nbtor_refined 0.183
r_mcbond_it 2.118
r_dihedral_angle_1_deg 7.253
r_xyhbond_nbd_refined 0.185
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1948
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 158

Software

Software
Software Name Purpose
SCALEPACK data scaling
PDB_EXTRACT data extraction version: 1.601
HKL-2000 data reduction
SOLVE phasing
REFMAC refinement version: 5.2.0019