2QYV | pdb_00002qyv

Crystal structure of putative Xaa-His dipeptidase (YP_718209.1) from Haemophilus somnus 129PT at 2.11 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.9	277	NANODROP, 2.0M (NH4)2SO4, 5.0% Isopropanol, 0.1M Citrate pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.17	70.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.922	α = 90
b = 84.293	β = 90
c = 123.204	γ = 90

Symmetry
Space Group	P 21 21 2

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 collimating mirror, toroid focusing mirror	2007-06-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97920, 0.91837, 0.97908	SSRL	BL9-2

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	2.11	47.836	98.1	0.086	0.086	8.2	3.8		102365			30.01

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)
1	2.11	2.22	99.4		0.584	0.584	1.3	3.8	15031

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	2.11	47.836	102314	5107	97.68	0.221	0.221	0.22	0.23	0.244	0.25	RANDOM	47.21

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]
-2.02			3.6		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.759
r_dihedral_angle_4_deg	17.546
r_dihedral_angle_3_deg	15.159
r_dihedral_angle_1_deg	6.414
r_scangle_it	3.932
r_scbond_it	2.803
r_mcangle_it	2.242
r_mcbond_it	1.446
r_angle_refined_deg	1.271
r_angle_other_deg	0.828
r_mcbond_other	0.375
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.186
r_nbd_other	0.184
r_symmetry_hbond_refined	0.174
r_nbtor_refined	0.173
r_symmetry_vdw_other	0.164
r_xyhbond_nbd_refined	0.151
r_nbtor_other	0.085
r_chiral_restr	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7212
Nucleic Acid Atoms
Solvent Atoms	466
Heterogen Atoms	208

Software

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