6PE3 | pdb_00006pe3

Structure of YcaO enzyme from Methanocaldococcus jannaschii in complex with ATP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		282	0.1 M sodium acetate pH 4.6, 2.0 M ammonium sulfate, 0.02 M taurine

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.841	α = 90
b = 106.841	β = 90
c = 182.556	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS EIGER X 9M		2017-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.979106	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	25.6	95.61	19.9	30.1		26776

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	25	25367	1391	95.61	0.20352	0.20111	0.2	0.25054	0.25	RANDOM	68.259

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]
1.69	0.84		1.69		-5.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.941
r_dihedral_angle_3_deg	17.232
r_dihedral_angle_4_deg	14.4
r_long_range_B_refined	9.783
r_dihedral_angle_1_deg	6.183
r_mcangle_it	5.661
r_scbond_it	4.938
r_mcbond_it	3.867
r_angle_refined_deg	1.531
r_chiral_restr	0.105
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2996
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
autoPROC	data scaling
PHENIX	phasing