6KM5 | pdb_00006km5

Human Carbonic Anhydrase II native 13 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	7.8	293	1.3 M sodium citrate, 100 mM Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.172	α = 90
b = 41.32	β = 104.073
c = 71.993	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		2019-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.8856	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.15	30	99.4	0.049	33.05	6.6		84743

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.17			0.436	4.78

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	1.151	29.07	84726	4109	99.298	0.104	0.1028	0.1	0.1288	0.13	16.179

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]
-0.002			0.009		-0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.661
r_dihedral_angle_2_deg	33.823
r_dihedral_angle_4_deg	20.853
r_dihedral_angle_3_deg	12.615
r_sphericity_bonded	12.302
r_rigid_bond_restr	6.957
r_dihedral_angle_1_deg	6.716
r_lrange_it	5.46
r_lrange_other	4.808
r_scangle_it	3.922
r_scangle_other	3.921
r_scbond_it	3.434
r_scbond_other	3.434
r_mcangle_other	2.666
r_mcangle_it	2.639
r_angle_refined_deg	2.455
r_mcbond_it	2.035
r_mcbond_other	1.84
r_angle_other_deg	1.729
r_nbd_other	0.341
r_symmetry_nbd_refined	0.31
r_nbd_refined	0.298
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.186
r_chiral_restr	0.165
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.124
r_symmetry_nbtor_other	0.079
r_metal_ion_refined	0.066
r_bond_refined_d	0.03
r_gen_planes_refined	0.014
r_gen_planes_other	0.013
r_symmetry_xyhbond_nbd_other	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	13

Software

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