1K7C

Rhamnogalacturonan acetylesterase with seven N-linked carbohydrate residues distributed at two N-glycosylation sites refined at 1.12 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DEO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298Li2SO4, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
1.8543.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.17α = 90
b = 56.92β = 90
c = 71.69γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray263IMAGE PLATEMARRESEARCHmirrors1997-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B1.1024EMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.123897.7644629644629
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.121.1482.10.37

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRFREE R1DEO1.12408056871116401997.80.10950.10450.10330.1344RANDOM
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
1617062123.96
RMS Deviations
KeyRefinement Restraint Deviation
s_anti_bump_dis_restr0.195
s_non_zero_chiral_vol0.106
s_approx_iso_adps0.103
s_zero_chiral_vol0.079
s_similar_adp_cmpnt0.041
s_angle_d0.031
s_from_restr_planes0.0264
s_similar_dist0.024
s_rigid_bond_adp_cmpnt0.022
s_bond_d0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1735
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms106

Software

Software
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement