2QDP | pdb_00002qdp

Crystal structure of the HePTP catalytic domain C270S mutant crystallized in ammonium acetate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZC0	PDB ENTRY 1ZC0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.07 M AMMONIUM ACETATE, 0.07 M BIS-TRIS, 12% POLYETHYLENE GLYCOL 10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.18	70.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.131	α = 90
b = 127.131	β = 90
c = 60.538	γ = 120

Symmetry
Space Group	P 61

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	ADSC QUANTUM 4	Si(111) CHANNEL CUT MONOCHROMATOR, OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR	2006-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9795	NSLS	X6A

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	2.72	50	99.2	0.122	6.6	4.2	15103	14980	1	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	2.72	2.82	98.4		0.601		4.1

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 (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 1ZC0	2.72	20	14410	14314	752	99.33	0.16055	0.15709	0.15	0.22681	0.22	RANDOM	28.506

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]
-0.25	-0.12		-0.25		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.231
r_dihedral_angle_4_deg	21.046
r_dihedral_angle_3_deg	17.817
r_scangle_it	10.128
r_scbond_it	7.5
r_dihedral_angle_1_deg	7.055
r_mcangle_it	4.555
r_mcbond_it	2.862
r_angle_refined_deg	2
r_nbtor_refined	0.329
r_nbd_refined	0.239
r_symmetry_hbond_refined	0.204
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.123
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
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_refined
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	2299
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	5

Software

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