8VQ7 | pdb_00008vq7

hCA-II-apo structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MHL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	2.1 M Malonate, Tris, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.431	α = 90
b = 41.283	β = 104.378
c = 72.758	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	PIXEL	DECTRIS EIGER X 16M		2019-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

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	1.409	41.28	98.8	0.177	0.206	0.103	0.948	9.3	4.5		46783

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.43	94		0.18	4.5	4.1

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	THROUGHOUT	1.409	41.136	46641	2280	98.465	0.135	0.1334	0.1329	0.1724	0.1737	13.543

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]
-1.227		0.466	-0.64		1.439

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.649
r_dihedral_angle_3_deg	12.44
r_dihedral_angle_1_deg	6.829
r_dihedral_angle_2_deg	4.858
r_lrange_it	3.675
r_rigid_bond_restr	3.52
r_lrange_other	2.914
r_scangle_it	1.844
r_scangle_other	1.844
r_angle_refined_deg	1.651
r_mcangle_it	1.64
r_mcangle_other	1.639
r_scbond_it	1.363
r_scbond_other	1.363
r_mcbond_it	1.109
r_mcbond_other	1.108
r_angle_other_deg	0.59
r_nbd_refined	0.194
r_symmetry_xyhbond_nbd_refined	0.194
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_other	0.185
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.166
r_nbd_other	0.158
r_xyhbond_nbd_refined	0.145
r_metal_ion_refined	0.107
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.083
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
REFMAC	phasing