2CE6 | pdb_00002ce6

Structure of Helix Pomatia agglutinin with no ligands

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			HANGING DROP METHOD WITH PRECIPITATION SOLUTION CONTAINING LITHIUM SULPHATE (2 M) AND AMMONIUM SULPHATE (3.5 M) IN SODIUM CITRATE BUFFER (1.5M, PH 6.5).

Crystal Properties
Matthews coefficient	Solvent content
2.53	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 61.6	β = 90
c = 105	γ = 120

Symmetry
Space Group	P 63 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 CCD	MIRROR	2002-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.4	52.49	99.8	0.07	22.67	7.35		5042			56

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	2.4	2.43	99.8		0.38	2.59	4.37

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 ENTRY 2CCV	2.4	47.57	4785	236	99.6	0.224	0.222	0.22	0.266	0.28	RANDOM	52.99

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]
-2.02	-1.01		-2.02		3.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.573
r_dihedral_angle_4_deg	23.151
r_dihedral_angle_3_deg	15.467
r_dihedral_angle_1_deg	5.9
r_scangle_it	2.058
r_angle_refined_deg	1.458
r_scbond_it	1.335
r_mcangle_it	0.991
r_mcbond_it	0.804
r_angle_other_deg	0.787
r_symmetry_vdw_other	0.205
r_nbd_other	0.196
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.182
r_nbtor_refined	0.178
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.168
r_nbtor_other	0.088
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
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	780
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

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