3M5Q

0.93 A Structure of Manganese-Bound Manganese Peroxidase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529820% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5, Vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5451.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.57α = 90
b = 45.3β = 97.31
c = 52.83γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plate1999-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.08SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
10.93160930.06626.34.92649581.42
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
0.930.95930.5121.92

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R1YYD0.93842243170191300396796.70.1240.1070.134RANDOM13.927
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]
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.112
s_non_zero_chiral_vol0.106
s_zero_chiral_vol0.096
s_anti_bump_dis_restr0.062
s_similar_adp_cmpnt0.05
s_angle_d0.033
s_from_restr_planes0.028
s_bond_d0.018
s_rigid_bond_adp_cmpnt0.007
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2629
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms91

Software

Software
Software NamePurpose
SHELXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
SHELXL-97refinement