6IM3 | pdb_00006im3

Crystal structure of a highly thermostable carbonic anhydrase from Persephonella marina EX-H1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EKI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	100 mM glycine pH 9.5, 28-32% (w/v) polyethylene glycol (PEG) 400, and 200-400 mM calcium chloride dehydrate, 7 mM acetazolamide

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.04	α = 90
b = 120.811	β = 90
c = 123.915	γ = 90

Symmetry
Space Group	P 21 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	77	CCD	ADSC QUANTUM 270		2018-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1.0	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	123.92	99.2	0.033	0.995	42.4	9.2		113905

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07			0.445	0.788

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	6EKI	2	123.92	113905	5968	98.67	0.21096	0.20949	0.22	0.23971	0.25	RANDOM	55.607

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]
1.9			1.26		-3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.587
r_dihedral_angle_3_deg	16.011
r_dihedral_angle_4_deg	13.94
r_long_range_B_refined	11.695
r_long_range_B_other	11.684
r_scangle_other	9.432
r_scbond_it	6.58
r_scbond_other	6.58
r_mcangle_other	6.489
r_mcangle_it	6.488
r_dihedral_angle_1_deg	6.239
r_mcbond_it	5.013
r_mcbond_other	5.012
r_angle_refined_deg	2.167
r_angle_other_deg	1.563
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.01
r_gen_planes_other	0.009
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10818
Nucleic Acid Atoms
Solvent Atoms	472
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing