X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details The native recombinant PGIS (25 mg/ml in the buffer containing 20 mM Tris, pH 8.0 and 150 mM NaCl) was found to crystallize spontaneously into needle clusters in the Eppendorf tube when stored at 4 C for about a week. A combination of microseeding technique and the hanging-drop vapor-diffusion method was then used to improve crystal quality. Specifically, seed stock was prepared by crushing these initial PGIS needle clusters with the Seed Bead Kit (Hampton Research). Following four 10-fold serial dilutions of the seed stock using the gel filtration buffer, 1 micro-l of diluted seeds was added into a 10 micro-l drop of freshly concentrated PGIS sample, and equilibrated at 4 C against 450 micro-l of the gel filtration buffer. High quality single crystals of PGIS were most often obtained using 100- or 1000-fold diluted seed stock, and reached suitable size (~ 0.05,0.05 ~ 0.1 mm3) within one week., VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.73 α = 90
b = 105.6 β = 92.01
c = 73.95 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-05-15
CCD ADSC QUANTUM 315 -- 2006-06-29
Diffraction Radiation
Monochromator Protocol
-- MAD
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.9537, 0.9793 SPRING-8 BL12B2
SYNCHROTRON NSRRC BEAMLINE BL13B1 0.980127 NSRRC BL13B1

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
2.15 30 90.9 -- 0.063 -- 2.8 56459 51322 -- -- --
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)
2.15 2.23 93.5 -- 0.35 3.1 -- --

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 2.15 20.15 -- -- -- 48702 2601 90.96 -- 0.20407 0.2009 0.26313 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 2.151 2.206 -- 195 3616 0.215 0.318 -- 93.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.948
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.987
r_scbond_it 1.961
r_mcangle_it 1.213
r_mcbond_it 0.642
r_nbd_refined 0.205
r_gen_planes_refined 0.005
r_chiral_restr 0.095
r_dihedral_angle_4_deg 18.433
r_dihedral_angle_3_deg 17.588
r_dihedral_angle_2_deg 32.256
r_dihedral_angle_1_deg 6.177
r_angle_refined_deg 1.38
r_bond_refined_d 0.011
r_nbtor_refined 0.304
r_xyhbond_nbd_refined 0.16
r_symmetry_vdw_refined 0.192
r_symmetry_hbond_refined 0.154
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7611
Nucleic Acid Atoms 0
Heterogen Atoms 87
Solvent Atoms 435

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement