2PRR | pdb_00002prr

Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.1	277	NANODROP, 0.2M Na2HPO4, 20.0% PEG 3350, No Buffer pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.105	α = 84.26
b = 93.953	β = 81.64
c = 120.898	γ = 77.73

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2006-12-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97932, 0.97905	SSRL	BL11-1

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	1.88	48.912	87.2	0.079	6.23			211872			30.222

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	1.88	1.95	77.4		0.419	2		18037

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.15	48.912	152688	7726	94.68	0.213	0.213	0.211	0.21	0.262	0.26	RANDOM	32.806

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]
0.94	-2.42	-2.97	-0.85	4.05	0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.13
r_dihedral_angle_4_deg	11.107
r_dihedral_angle_3_deg	10.693
r_scangle_it	6.123
r_scbond_it	4.919
r_dihedral_angle_1_deg	3.232
r_mcangle_it	2.393
r_angle_refined_deg	1.535
r_mcbond_it	1.523
r_angle_other_deg	0.96
r_mcbond_other	0.681
r_xyhbond_nbd_refined	0.231
r_symmetry_hbond_refined	0.224
r_nbd_refined	0.213
r_symmetry_vdw_other	0.196
r_nbtor_refined	0.184
r_nbd_other	0.162
r_symmetry_vdw_refined	0.109
r_chiral_restr	0.093
r_nbtor_other	0.089
r_xyhbond_nbd_other	0.052
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17690
Nucleic Acid Atoms
Solvent Atoms	1338
Heterogen Atoms	245

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing