4MFG | pdb_00004mfg

2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 12.5mM Suberic acid, 12.5mM Sebcic acid, 12.5mM Hexadecanedioic acid, 12.5mM Dodecanedioic acid, 40% Ethanol, 0.1M Hepes pH 7.5, 2% MPD, 20% (w/v) PEG 3350; Cryo: paratone., VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.089	α = 90
b = 127.089	β = 90
c = 76.732	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	Beryllium lenses	2011-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	30	99.9	0.107	29.5	9.7	47926	47926		-3	19.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	100		0.61	3.8	9.5	2398

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1XHD	2	29.36	45299	45299	2416	99.87	0.21439	0.21439	0.21158	0.22	0.26663	0.27	RANDOM	42.179

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]
0.89	0.45		0.89		-2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.44
r_dihedral_angle_4_deg	12.229
r_dihedral_angle_3_deg	11.971
r_long_range_B_refined	6.838
r_long_range_B_other	6.628
r_dihedral_angle_1_deg	3.762
r_scangle_other	3.322
r_scbond_it	2.412
r_scbond_other	2.397
r_mcangle_it	2.199
r_mcangle_other	2.198
r_angle_refined_deg	1.619
r_mcbond_it	1.506
r_mcbond_other	1.505
r_angle_other_deg	0.785
r_chiral_restr	0.102
r_gen_planes_refined	0.018
r_gen_planes_other	0.017
r_bond_refined_d	0.012
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5152
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	6

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing