2C4D | pdb_00002c4d

2.6A Crystal Structure of Psathyrella velutina Lectin in Complex with N-acetylglucosamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BWM	PDB ENTRY 2BWM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		2.2M AMMONIUM SULPHATE 0.1M MES PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.767	α = 90
b = 106.767	β = 90
c = 86.622	γ = 120

Symmetry
Space Group	P 31 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	MARRESEARCH	MIRRORS	2005-04-14	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	2.5	25.64	99.9	0.1	5.47	11.13		17901			63.3

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	2.6	2.67	100		0.47	1.57	11.29

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 2BWM	2.6	92.45	16965	912	99.9	0.205	0.202	0.21	0.271	RANDOM	43.25

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]
1.39	0.7		1.39		-2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.341
r_dihedral_angle_3_deg	15.567
r_dihedral_angle_4_deg	11.874
r_dihedral_angle_1_deg	6.785
r_scangle_it	2.627
r_angle_refined_deg	1.722
r_scbond_it	1.718
r_mcangle_it	1.23
r_angle_other_deg	0.841
r_mcbond_it	0.712
r_symmetry_vdw_other	0.227
r_nbd_refined	0.198
r_nbd_other	0.198
r_symmetry_vdw_refined	0.193
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.171
r_symmetry_hbond_refined	0.123
r_chiral_restr	0.089
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	3038
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	111

Software

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