2H98 | pdb_00002h98

Crystal structure of the effector binding domain of a CatM variant, CatM(V158M)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F7B	PDB accession code 2F7B, CatM-EBD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			296.4	Precipitant:0.1 M LiCL, 0.1 M MES, 40% PEG8000 Protein: 20 mM tris HCl, 0.5 M NaCl, 250 mM imidazole, pH 7.9, 10% glycerol Equal volumes mixed, Microbatch under oil. The growing crystallization solution was in pH 6 and the protein solution was in pH 7.9 condition, temperature 296.4K

Crystal Properties
Matthews coefficient	Solvent content
2	37.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.447	α = 69.55
b = 51.038	β = 89.51
c = 59.12	γ = 77.63

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	CCD	MARRESEARCH		2004-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97934	APS	19-BM

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	1.8	50	94.5	0.045	9.4	1.6	56879	34934

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	1.8	1.86	89.87	93	0.346	14.3	1.6	5173

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 accession code 2F7B, CatM-EBD	1.8	44.2	34930	33175	1755	94.24	0.171	0.171	0.167	0.2182	0.232	0.2682	RANDOM	8.918

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]
-0.22	-0.68	0.76	1.5	-0.86	-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.409
r_dihedral_angle_4_deg	14.737
r_dihedral_angle_3_deg	11.456
r_dihedral_angle_1_deg	5.674
r_scangle_it	3.153
r_scbond_it	2.328
r_mcangle_it	1.126
r_angle_refined_deg	1.067
r_mcbond_it	0.776
r_angle_other_deg	0.744
r_nbd_refined	0.182
r_symmetry_vdw_other	0.169
r_nbtor_refined	0.164
r_nbd_other	0.159
r_symmetry_hbond_refined	0.126
r_xyhbond_nbd_refined	0.115
r_symmetry_vdw_refined	0.104
r_mcbond_other	0.085
r_nbtor_other	0.077
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3404
Nucleic Acid Atoms
Solvent Atoms	719
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling