3EYX | pdb_00003eyx

Crystal structure of Carbonic Anhydrase Nce103 from Saccharomyces cerevisiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DDZ	PDB ENTRY 1DDZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	289	20% PEG 4000, 0.2M sodium acetate, 0.1M sodium citrate, 20% ethylene glycol , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.57	α = 90
b = 155.73	β = 90
c = 89.69	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.03	30	93.1	0.066	0.081	13.5	2.8	71916	25657

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.03	2.14	81		0.31	0.383	3.2	2.8

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	PDB ENTRY 1DDZ	2.04	16.11	24369	1288	94.17	0.19912	0.19689	0.2	0.2413	0.24	RANDOM	21.718

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]
-0.85			0.9		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.755
r_dihedral_angle_4_deg	15.433
r_dihedral_angle_3_deg	12.668
r_dihedral_angle_1_deg	5.004
r_scangle_it	2.226
r_scbond_it	1.575
r_angle_refined_deg	1.107
r_mcangle_it	0.923
r_mcbond_it	0.778
r_nbtor_refined	0.292
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.185
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.078
r_metal_ion_refined	0.031
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3130
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	26

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling