3E85

Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Diphenylurea

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QIM	PDB entry 2QIM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	292	1.4 M Sodium citrate, 0.1 M citrate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.362	α = 90
b = 73.256	β = 90
c = 99.956	γ = 90

Symmetry
Space Group	C 2 2 21

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	MAR CCD 165 mm	mirrors	2005-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.81	EMBL/DESY, HAMBURG	X11

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	1.95	40	99.56	0.075	20.8	5.7		9529		-3	37.9

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	1.95	2.02	96.8		0.398	3.8	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2QIM	1.95	15	8631	860	99.54	0.19323	0.18788	0.2465	RANDOM	30.611

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]
-1.66			-1.34		3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.895
r_dihedral_angle_3_deg	16.875
r_scangle_it	6.456
r_dihedral_angle_1_deg	6.214
r_dihedral_angle_4_deg	5.89
r_scbond_it	4.229
r_angle_refined_deg	1.878
r_mcangle_it	1.85
r_mcbond_it	1.044
r_angle_other_deg	0.941
r_nbd_refined	0.244
r_mcbond_other	0.241
r_symmetry_hbond_refined	0.217
r_nbd_other	0.211
r_nbtor_refined	0.195
r_metal_ion_refined	0.192
r_symmetry_vdw_refined	0.157
r_xyhbond_nbd_refined	0.152
r_symmetry_vdw_other	0.144
r_chiral_restr	0.106
r_nbtor_other	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1155
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing