6GQI | pdb_00006gqi

Thermocrispum municipale cyclohexanone monooxygenase bound to hexanoic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M10

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293	100 mM Tris-HCl, 30 % PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.069	α = 90
b = 93.69	β = 90
c = 159.639	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 PILATUS3 S 6M		2017-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.97625	ESRF	ID30B

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	2	44.4	99.7	0.148	0.993	6.7	4.2		65972

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	2	2.05	99.6		0.8	0.65	1.7	4.2

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	5M10	2	44.4	62601	3307	98.74	0.14178	0.13878	0.15	0.19946	0.21	RANDOM	23.505

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]
0.27			-0.46		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.843
r_sphericity_free	34.347
r_dihedral_angle_4_deg	16.838
r_dihedral_angle_3_deg	14.687
r_sphericity_bonded	13.017
r_dihedral_angle_1_deg	6.72
r_long_range_B_refined	5.738
r_long_range_B_other	5.602
r_scangle_other	5.517
r_rigid_bond_restr	5.374
r_scbond_it	4.778
r_scbond_other	4.778
r_mcangle_it	4.549
r_mcangle_other	4.548
r_mcbond_it	3.858
r_mcbond_other	3.839
r_angle_refined_deg	2.197
r_angle_other_deg	1.189
r_chiral_restr	0.131
r_bond_refined_d	0.024
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8288
Nucleic Acid Atoms
Solvent Atoms	800
Heterogen Atoms	230

Software

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