6VCF | pdb_00006vcf

Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, iron form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	22% Sokalan PA 25 CL 0.1 M MES-NaOH pH 6 0.1 M NaCl 22% Xylitol

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.267	α = 90
b = 107.267	β = 90
c = 491.109	γ = 120

Symmetry
Space Group	P 61

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		2019-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979354	NSLS-II	17-ID-2

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	2.68	50	99.5	0.185	0.999	11.77	10.5		88233			66

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	2.68	2.85	97.5		1.954	0.373	0.97	10.1

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 (All)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3KVC	2.687	49.149	88143	4373	99.741	0.253	0.2516	0.2714	83.729

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]
-0.846	-0.423		-0.846		2.744

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.277
r_dihedral_angle_4_deg	13.863
r_dihedral_angle_3_deg	12.868
r_dihedral_angle_1_deg	7.075
r_lrange_it	2.077
r_lrange_other	2.066
r_angle_refined_deg	1.198
r_angle_other_deg	1.051
r_mcangle_it	0.831
r_mcangle_other	0.831
r_scangle_it	0.493
r_scangle_other	0.493
r_mcbond_it	0.45
r_mcbond_other	0.45
r_scbond_it	0.267
r_scbond_other	0.267
r_symmetry_xyhbond_nbd_refined	0.211
r_nbd_refined	0.17
r_metal_ion_refined	0.162
r_nbtor_refined	0.159
r_nbd_other	0.157
r_symmetry_nbd_other	0.153
r_xyhbond_nbd_refined	0.131
r_symmetry_nbd_refined	0.11
r_ncsr_local_group_2	0.071
r_ncsr_local_group_1	0.068
r_symmetry_nbtor_other	0.067
r_ncsr_local_group_10	0.066
r_ncsr_local_group_7	0.062
r_ncsr_local_group_4	0.06
r_ncsr_local_group_13	0.059
r_ncsr_local_group_5	0.053
r_ncsr_local_group_3	0.052
r_ncsr_local_group_14	0.051
r_ncsr_local_group_9	0.048
r_ncsr_local_group_6	0.044
r_ncsr_local_group_8	0.044
r_ncsr_local_group_12	0.041
r_ncsr_local_group_11	0.04
r_ncsr_local_group_15	0.037
r_chiral_restr	0.036
r_xyhbond_nbd_other	0.032
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21385
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing