2JDZ | pdb_00002jdz

Crystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H9P	PDB ENTRY 1H9P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 30% PEG 400, 0.1M MES, PH 6.5 AND 0.1M CDCL2.

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.222	α = 90
b = 89.222	β = 90
c = 106.069	γ = 90

Symmetry
Space Group	I 41 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	MARRESEARCH		2005-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	2.1	34.1	99.9	0.08	5.6	10.4		12834		2

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	2.1	2.21	100		0.3	2.1	10.6

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1H9P	2.1	34.14	11848	971	99.8	0.2	0.196	0.2	0.249	RANDOM	31.16

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]
0.12			0.12		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.409
r_dihedral_angle_4_deg	24.511
r_dihedral_angle_3_deg	16.619
r_dihedral_angle_1_deg	7.19
r_scangle_it	3.483
r_scbond_it	2.271
r_angle_refined_deg	1.658
r_mcangle_it	1.452
r_mcbond_it	0.833
r_symmetry_hbond_refined	0.405
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.272
r_xyhbond_nbd_refined	0.229
r_nbd_refined	0.202
r_chiral_restr	0.112
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1761
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing