9GVA | pdb_00009gva

Crystal structure of the gamma carbonic anhydrase from Porphyromonas gingivalis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q7MV79-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	296	2.0 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 2% v/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.752	α = 90
b = 120.752	β = 90
c = 91.31	γ = 120

Symmetry
Space Group	P 65

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 PILATUS 6M		2024-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

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	2.4	45.37	95.9	0.13	0.139	0.049	0.999	18.5	15.3		28525

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	2.4	2.49	100		0.77	0.823	0.289	0.928	4.4	15.7

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	2.4	45.37	28494	1452	95.917	0.167	0.1654	0.1753	0.1965	0.1991	38.701

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]
0.553	0.277		0.553		-1.795

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.79
r_dihedral_angle_3_deg	17.895
r_dihedral_angle_4_deg	15.284
r_lrange_it	10.346
r_lrange_other	10.336
r_scangle_it	8.068
r_scangle_other	8.067
r_dihedral_angle_1_deg	7.855
r_mcangle_it	5.419
r_mcangle_other	5.418
r_scbond_it	5.361
r_scbond_other	5.361
r_mcbond_it	3.737
r_mcbond_other	3.736
r_angle_refined_deg	1.77
r_angle_other_deg	1.327
r_symmetry_nbd_refined	0.275
r_nbd_other	0.232
r_symmetry_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.194
r_nbd_refined	0.186
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.141
r_metal_ion_refined	0.089
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3925
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	3

Software

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