2REX | pdb_00002rex

Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CLS	PDB entries 2CLS,2R2O
experimental model	PDB	2R2O	PDB entries 2CLS,2R2O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.136	α = 90
b = 71.653	β = 128.36
c = 101.885	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 270		2007-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91790	CHESS	F1

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	2.3	30	97.3	0.06	9.1	3.7		36932

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	2.3	2.38	84.8		0.231		3.2	3232

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 entries 2CLS,2R2O	2.3	20	36863	36863	999	97.472	0.216	0.216	0.215	0.26	0.248	0.28	Thin shells	28.565

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]
5.87		2.92	-2.831		0.585

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.303
r_dihedral_angle_4_deg	22.082
r_dihedral_angle_3_deg	14.752
r_dihedral_angle_1_deg	6.345
r_scangle_it	2.327
r_scbond_it	1.508
r_angle_refined_deg	1.448
r_angle_other_deg	0.949
r_mcangle_it	0.936
r_mcbond_it	0.595
r_symmetry_vdw_refined	0.4
r_symmetry_vdw_other	0.197
r_metal_ion_refined	0.196
r_nbd_refined	0.191
r_nbd_other	0.19
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.143
r_mcbond_other	0.128
r_symmetry_hbond_refined	0.124
r_nbtor_other	0.087
r_chiral_restr	0.081
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4279
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	98

Software

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