7Q0C | pdb_00007q0c

Mimic carbonic anhydrase IX in complex with Methyl 2-chloro-4-(cyclohexylsulfanyl)-5-sulfamoylbenzoate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Crystallization buffer: 0.1M sodium bicine (pH 9.0), 0.2 M ammonium sulfate and 2M sodium malonate (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.06	α = 90
b = 41.348	β = 104.14
c = 72.029	γ = 90

Symmetry
Space Group	P 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		2013-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9755	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.12	41.35	81.3	0.042	0.063	0.032	18.9	3.8		146352

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.122	1.18	51.4		0.102	0.102	0.153	0.079	6.7	3.6

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 (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	3HLJ	1.12	41.35	131858	14494	81.32	0.1637	0.1603	0.16	0.1937	0.19	RANDOM	18.286

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]
1.47	1.03	-0.41	-0.41	0.96	-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.027
r_sphericity_free	28.405
r_sphericity_bonded	25.223
r_rigid_bond_restr	20.997
r_dihedral_angle_4_deg	20.67
r_dihedral_angle_3_deg	14.895
r_dihedral_angle_1_deg	7.172
r_angle_refined_deg	2.532
r_chiral_restr	0.52
r_bond_refined_d	0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.027
r_sphericity_free	28.405
r_sphericity_bonded	25.223
r_rigid_bond_restr	20.997
r_dihedral_angle_4_deg	20.67
r_dihedral_angle_3_deg	14.895
r_dihedral_angle_1_deg	7.172
r_angle_refined_deg	2.532
r_chiral_restr	0.52
r_bond_refined_d	0.02
r_gen_planes_refined	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4079
Nucleic Acid Atoms
Solvent Atoms	602
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing
Coot	model building

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.