6KM4 | pdb_00006km4

Human Carbonic Anhydrase II native 07 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	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.18	α = 90
b = 41.317	β = 104.036
c = 72.225	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	97.9	0.054	26.01	6.6		84284

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			0.395	5.53

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	1.15	29.074	84072	4090	97.902	0.099	0.098	0.1	0.1242	0.12	14.62

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]
0.005			0.007		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	44.438
r_dihedral_angle_2_deg	34.314
r_dihedral_angle_4_deg	21.798
r_sphericity_bonded	12.451
r_dihedral_angle_3_deg	12.251
r_rigid_bond_restr	6.74
r_dihedral_angle_1_deg	6.633
r_lrange_it	4.979
r_scangle_it	4.786
r_scangle_other	4.785
r_lrange_other	4.44
r_scbond_it	3.927
r_scbond_other	3.927
r_mcangle_other	2.388
r_angle_refined_deg	2.368
r_mcangle_it	2.355
r_mcbond_it	1.747
r_mcbond_other	1.691
r_angle_other_deg	1.245
r_nbd_other	0.324
r_nbd_refined	0.301
r_symmetry_nbd_refined	0.298
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.185
r_chiral_restr	0.159
r_symmetry_xyhbond_nbd_refined	0.152
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.078
r_metal_ion_refined	0.061
r_symmetry_xyhbond_nbd_other	0.059
r_bond_refined_d	0.029
r_gen_planes_refined	0.014
r_gen_planes_other	0.005
r_bond_other_d	0.003

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