6LV4 | pdb_00006lv4

Co- Carbonic Anhydrase II pH 11.0 20 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
2.1	41.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.358	α = 90
b = 41.458	β = 104.02
c = 72.307	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	94.6	0.058	0.062	0.023	0.998	31.8	7.6		72173

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	91.2		0.424	0.455	0.165	0.922	5.6	7.6

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	72158	3699	94.594	0.114	0.1125	0.12	0.1394	0.15	13.542

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]
0.116		0.015	-0.111		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.976
r_dihedral_angle_2_deg	34.742
r_dihedral_angle_4_deg	23.27
r_sphericity_bonded	13.279
r_dihedral_angle_3_deg	11.944
r_dihedral_angle_1_deg	7.033
r_rigid_bond_restr	6.207
r_lrange_it	5.699
r_lrange_other	4.897
r_scangle_it	3.635
r_scangle_other	3.625
r_scbond_it	3.189
r_scbond_other	3.186
r_mcangle_other	3.039
r_mcangle_it	3.026
r_mcbond_it	2.562
r_angle_refined_deg	2.358
r_mcbond_other	2.27
r_angle_other_deg	1.187
r_symmetry_nbd_refined	0.31
r_nbd_refined	0.305
r_symmetry_xyhbond_nbd_other	0.302
r_nbd_other	0.256
r_metal_ion_refined	0.214
r_xyhbond_nbd_refined	0.206
r_chiral_restr	0.193
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.166
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.028
r_gen_planes_refined	0.014
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	17

Software

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