8A9M | pdb_00008a9m

Hippeastrum hybrid agglutinin, HHA, complex with beta-mannose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	50mM PBS, 2M Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.37	α = 90
b = 100.318	β = 137.27
c = 62.177	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	293	IMAGE PLATE	MAR scanner 300 mm plate		1993-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.8975	SRS	PX9.6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.2	23.82	98.5	0.133	0.148	0.063	0.986	8.2	4.9		15296

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	99.5		0.389	0.436	0.191	0.896		4.7

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	1MSA	2.2	23.82	14531	765	98.3	0.1691	0.1665	0.1757	0.2191	0.224	RANDOM	39.862

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]
-0.45		1.3	-5.34		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.674
r_dihedral_angle_3_deg	15.386
r_dihedral_angle_4_deg	11.191
r_dihedral_angle_1_deg	8.601
r_angle_refined_deg	1.474
r_angle_other_deg	1.218
r_chiral_restr	0.055
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1658
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction