2VE3 | pdb_00002ve3

Retinoic acid bound cyanobacterial CYP120A1

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		SUBSTRATE-FREE CYP120A1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		1.2 M SODIUM POTASSIUM TARTATE, 0.1 M MES PH6.5

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.46	α = 90
b = 132.97	β = 114.5
c = 67.42	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	20	95	0.1	9.6	2.9		62855		3	32.6

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	SUBSTRATE-FREE CYP120A1	2.1	19.85	61497	3238	95	0.225	0.223	0.22	0.267	0.27	RANDOM	27.95

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]
3.6		1.68	-1.69		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.797
r_dihedral_angle_4_deg	21.429
r_dihedral_angle_3_deg	16.78
r_dihedral_angle_1_deg	6.409
r_scangle_it	2.193
r_scbond_it	1.397
r_angle_refined_deg	1.37
r_mcangle_it	1.029
r_mcbond_it	0.595
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.208
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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_other
r_long_range_B_refined
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	6891
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	130

Software

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