8C9T | pdb_00008c9t

Catechol O-methyltransferase from Streptomyces avermitilis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DUW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1M MIB(Malonic acid,Imidazole,Boric acid) pH6.0; 25% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.457	α = 90
b = 168.744	β = 101.487
c = 57.242	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2022-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.5	46.71	96.2	0.051	0.999	22.6	7.1		131969

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53			0.278	0.967

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	46.71	131918	6583	96.071	0.168	0.1669	0.17	0.1936	0.2	14.486

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]
-0.356		-0.445	-0.57		1.023

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.893
r_dihedral_angle_4_deg	15.67
r_dihedral_angle_3_deg	12.487
r_dihedral_angle_1_deg	5.512
r_lrange_it	4.655
r_lrange_other	4.654
r_scangle_it	3.684
r_scangle_other	3.683
r_scbond_it	2.435
r_scbond_other	2.435
r_mcangle_other	2.055
r_mcangle_it	2.053
r_angle_refined_deg	1.825
r_angle_other_deg	1.563
r_mcbond_it	1.42
r_mcbond_other	1.411
r_symmetry_nbd_refined	0.269
r_nbd_refined	0.225
r_nbd_other	0.215
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.148
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6759
Nucleic Acid Atoms
Solvent Atoms	712
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing