9RAY | pdb_00009ray

Crystal structure of human carbonic anhydrase I in complex with N-benzyl-2-(2-chloro-N-(3-chloro-4-methoxyphenyl)acetamido)-2-(4-sulfamoylphenyl)acetamide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FIK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	296	1.5 M sodium citrate, 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.46	α = 90
b = 41.65	β = 104.421
c = 72.43	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 PILATUS 6M		2023-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.31	41.156	97.7	0.066	0.072	0.998	16.12	6.2		57876

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.34	97.1		0.722	0.789	0.852	2.94	6.2

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	NONE	1.31	41.156	57876	2815	97.754	0.2	0.1984	0.2064	0.2227	0.226	14.183

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]
-0.807		-0.381	0.689		0.278

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.226
r_dihedral_angle_4_deg	23.436
r_dihedral_angle_3_deg	14.268
r_dihedral_angle_1_deg	6.916
r_lrange_it	4.793
r_lrange_other	4.792
r_scangle_it	3.944
r_scangle_other	3.943
r_rigid_bond_restr	3.391
r_scbond_it	3.374
r_scbond_other	3.372
r_mcangle_other	3.08
r_mcangle_it	3.064
r_mcbond_it	2.3
r_mcbond_other	2.253
r_angle_refined_deg	2.025
r_angle_other_deg	1.528
r_symmetry_nbd_refined	0.243
r_nbd_refined	0.236
r_nbd_other	0.226
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_refined	0.088
r_metal_ion_refined	0.062
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2053
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing