6QFU | pdb_00006qfu

Human carbonic anhydrase II with bound IrCp* complex (cofactor 7) to generate an artificial transfer hydrogenase (ATHase)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZP9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	293	2.6 M ammonium sulfate, 50 mM Tris-H2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.038	α = 90
b = 41.264	β = 104.27
c = 71.9	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		2018-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	40.77	99.3	0.198	0.958	10.3	8		21112

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	99.9		1.026	0.386	7	8.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3ZP9	1.8	40.77	21112	1108	99.25	0.166	0.1649	0.18	0.1864	0.2	RANDOM	17.635

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]
0.32		0.62	-0.96		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.09
r_dihedral_angle_4_deg	21.177
r_dihedral_angle_3_deg	13.544
r_dihedral_angle_1_deg	7.277
r_mcangle_it	2.728
r_angle_refined_deg	2.665
r_angle_other_deg	2.346
r_mcbond_it	1.781
r_mcbond_other	1.776
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.09
r_dihedral_angle_4_deg	21.177
r_dihedral_angle_3_deg	13.544
r_dihedral_angle_1_deg	7.277
r_mcangle_it	2.728
r_angle_refined_deg	2.665
r_angle_other_deg	2.346
r_mcbond_it	1.781
r_mcbond_other	1.776
r_chiral_restr	0.087
r_bond_other_d	0.035
r_gen_planes_other	0.018
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2039
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.