6LV3 | pdb_00006lv3

Co- Carbonic Anhydrase II pH 11.0 0 atm CO2

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	11	293	1.3 M sodium citrate, 50 mM Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.33	α = 90
b = 41.259	β = 104.127
c = 72.083	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 270		2019-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.9793	PAL/PLS	7A (6B, 6C1)

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	1.2	30	95	0.085	0.091	0.033	0.995	23	7.6		71904

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	1.2	1.22	91.7		0.464	0.497	0.179	0.909	4.3	7.7

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5YUK	1.2	30	71822	3686	94.966	0.124	0.1229	0.13	0.1489	0.15	13.94

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]
-0.022		-0.07	0.032		0.023

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.488
r_dihedral_angle_2_deg	36.164
r_dihedral_angle_4_deg	24.712
r_dihedral_angle_3_deg	11.863
r_sphericity_bonded	10.853
r_dihedral_angle_1_deg	6.637
r_rigid_bond_restr	6.027
r_lrange_it	4.626
r_lrange_other	4.493
r_scangle_it	3.948
r_scangle_other	3.947
r_scbond_it	3.379
r_scbond_other	3.378
r_angle_refined_deg	2.484
r_mcangle_other	2.107
r_mcangle_it	2.055
r_mcbond_it	1.583
r_mcbond_other	1.456
r_angle_other_deg	1.309
r_symmetry_nbd_refined	0.336
r_nbd_other	0.336
r_nbd_refined	0.287
r_symmetry_xyhbond_nbd_refined	0.214
r_chiral_restr	0.211
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.156
r_metal_ion_refined	0.107
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.031
r_gen_planes_refined	0.015
r_bond_other_d	0.004
r_gen_planes_other	0.004
r_symmetry_xyhbond_nbd_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	7

Software

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