8RTV | pdb_00008rtv

Crystal structure of CYP154E1 from Thermobifida fusca YX in complex with 4-Phenylimidazole

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.334	α = 90
b = 97.176	β = 90
c = 135.688	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 16M		2021-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03319	PETRA III, DESY	P11

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	48.984	99.7	0.224	0.242	0.092	0.998	9.3	13		56184

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	2.05			2.09	2.272	0.882	0.475	1.2	12.4

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	NONE	2.002	48.984	56072	2787	99.618	0.221	0.2184	0.219	0.2714	0.271	34.445

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]
1.023			-0.454		-0.569

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.217
r_dihedral_angle_3_deg	14.034
r_dihedral_angle_2_deg	12.395
r_dihedral_angle_1_deg	7.982
r_lrange_it	6.968
r_lrange_other	6.965
r_scangle_it	5.616
r_scangle_other	5.616
r_mcangle_it	4.374
r_mcangle_other	4.374
r_scbond_it	3.82
r_scbond_other	3.819
r_mcbond_it	3.183
r_mcbond_other	3.183
r_angle_refined_deg	1.741
r_angle_other_deg	0.595
r_nbd_other	0.238
r_nbd_refined	0.221
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.153
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.151
r_ncsr_local_group_1	0.115
r_chiral_restr	0.086
r_metal_ion_refined	0.085
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6172
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	108

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
MOLREP	phasing
Coot	model building
XDS	data reduction
BUCCANEER	model building