7P6L | pdb_00007p6l

Heme domain of CYP505A30, a fungal hydroxylase from Myceliophthora thermophila, bound to dodecanoic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZOA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	0.1 M BICINE pH 8 10% PEG 1500 5 mM dodecanoic acid

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.49	α = 90
b = 171.49	β = 90
c = 175.647	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS EIGER2 XE 16M		2021-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.33	61.43	100	0.085	0.089	0.024	1	16.2	13.3		110041

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.38	100		4.01	4.174	1.154	0.296	0.2	13

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ZOA	2.33	61.43	106292	5477	99.99	0.2048	0.2033	0.2339	0.2003	RANDOM	83.184

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]
0.13			0.13		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.49
r_dihedral_angle_3_deg	17.318
r_dihedral_angle_4_deg	15.888
r_dihedral_angle_1_deg	7.048
r_angle_refined_deg	1.647
r_angle_other_deg	1.293
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14624
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	228

Software

Software
Software Name	Purpose
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction