3LFR

The Crystal Structure of a CBS Domain from a Putative Metal Ion Transporter Bound to AMP from Pseudomonas syringae to 1.55A


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 289.0
Details 25% PEG 3350, 0.1M Hepes PH 7.5, 0.2M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.15 α = 90
b = 50.65 β = 112.26
c = 51.87 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-08-12
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-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
1.53 50 99.2 0.102 -- -- 3.1 -- 33409 -- -- --
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)
1.55 1.61 99.7 0.652 -- -- 3.1 3299

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
-- 1.53 34.84 -- 0.0 -- 33130 1678 97.5 -- 0.177 0.175 0.212 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 1.534 1.574 -- 111 1994 0.203 0.281 -- 84.065
X Ray Diffraction 1.574 1.617 -- 106 2216 0.179 0.265 -- 96.952
X Ray Diffraction 1.617 1.664 -- 103 2207 0.166 0.237 -- 98.34
X Ray Diffraction 1.664 1.715 -- 109 2149 0.161 0.233 -- 98.259
X Ray Diffraction 1.715 1.771 -- 108 2106 0.164 0.218 -- 98.663
X Ray Diffraction 1.771 1.833 -- 110 2042 0.148 0.186 -- 99.216
X Ray Diffraction 1.833 1.902 -- 92 1979 0.157 0.227 -- 99.376
X Ray Diffraction 1.902 1.979 -- 112 1897 0.166 0.232 -- 99.752
X Ray Diffraction 1.979 2.067 -- 93 1825 0.171 0.205 -- 99.533
X Ray Diffraction 2.067 2.167 -- 90 1720 0.168 0.206 -- 99.341
X Ray Diffraction 2.167 2.284 -- 97 1657 0.161 0.226 -- 99.886
X Ray Diffraction 2.284 2.422 -- 81 1591 0.176 0.226 -- 99.642
X Ray Diffraction 2.422 2.588 -- 84 1470 0.193 0.254 -- 99.552
X Ray Diffraction 2.588 2.795 -- 75 1374 0.193 0.228 -- 99.451
X Ray Diffraction 2.795 3.059 -- 77 1253 0.187 0.259 -- 99.254
X Ray Diffraction 3.059 3.417 -- 58 1165 0.174 0.189 -- 99.918
X Ray Diffraction 3.417 3.939 -- 60 1017 0.157 0.155 -- 99.08
X Ray Diffraction 3.939 4.809 -- 44 846 0.162 0.185 -- 96.634
X Ray Diffraction 4.809 6.738 -- 40 657 0.21 0.177 -- 96.271
X Ray Diffraction 6.738 34.841 -- 28 287 0.223 0.248 -- 73.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.994
Anisotropic B[1][1] -0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.13
Anisotropic B[2][2] 0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.09
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.011
r_chiral_restr 0.091
r_rigid_bond_restr 1.417
r_scbond_it 3.012
r_mcangle_it 1.891
r_angle_refined_deg 1.481
r_scangle_it 4.539
r_gen_planes_refined 0.007
r_dihedral_angle_3_deg 11.311
r_dihedral_angle_4_deg 15.901
r_mcbond_it 1.129
r_dihedral_angle_1_deg 5.387
r_dihedral_angle_2_deg 36.421
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1953
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 172

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: refmac_5.5.0102
PDB_EXTRACT data extraction version: 3.004
SBC-Collect data collection
HKL-3000 data reduction
HKL-3000 data scaling
HKL-3000 phasing
SHELX phasing
MLPHARE phasing
DM phasing
ARP/wARP model building
Coot model building