3Q3J | pdb_00003q3j

Crystal structure of plexin A2 RBD in complex with Rnd1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2REX	pdb entries 2REX, 3ig3
experimental model	PDB	3IG3	pdb entries 2REX, 3ig3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	vapor diffusion, sitting drops	7.5	293	The complex sample (2.7 mg/mL) was incubated with 5mM Gpp(NH)p. Crystallization cocktail: 25.5% PEG3350, 0.2 M magnesium chloride, 0.1M Hepes. Seeding was applied in the production of the diffraction-quality crystal., pH 7.5, vapor diffusion, sitting drops, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.022	α = 90
b = 67.129	β = 90
c = 145.291	γ = 90

Symmetry
Space Group	I 2 2 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	ADSC QUANTUM 315		2010-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98322	APS	19-ID

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	1.97	40	99.9	0.07	11.7	7.2		20734

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)
	1.97	2	100		0.964		7.2	1018

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 (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 2REX, 3ig3	1.971	39.276	20667	1072	99.284	0.213	0.211	0.2143	0.2479	0.2454	RANDOM	30.452

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]
-0.595			0.241		0.354

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.949
r_dihedral_angle_4_deg	21.304
r_dihedral_angle_3_deg	12.195
r_dihedral_angle_1_deg	5.593
r_scangle_it	2.383
r_scbond_it	1.512
r_angle_refined_deg	1.195
r_mcangle_it	0.938
r_angle_other_deg	0.873
r_mcbond_it	0.491
r_mcbond_other	0.118
r_chiral_restr	0.07
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2065
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling