1ZGS | pdb_00001zgs

Parkia platycephala seed lectin in complex with 5-bromo-4-chloro-3-indolyl-a-D-mannose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	2.0M ammonium dihydrogen phosphate, 0.1M Tris-hydrochloride, 3mM, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.3	61.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.239	α = 90
b = 114.177	β = 119.88
c = 80.304	γ = 90

Symmetry
Space Group	P 1 21 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		2004-09-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.91995, 0.91932, 0.92191	ESRF	BM16

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	69.673	100	0.048	0.04	15.3	5.8	43436	43436	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.64	100		0.17	0.138	2.3	5.8	6288

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	THROUGHOUT	2.5	30	2	43403	39474	3929	99.99	0.2117	0.2117	0.2085	0.21	0.24387	0.24	RANDOM	25.301

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]
0.43		0.88	-0.07		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.847
r_dihedral_angle_4_deg	18.92
r_dihedral_angle_3_deg	18.694
r_dihedral_angle_1_deg	7.273
r_scangle_it	3.793
r_angle_refined_deg	3.16
r_scbond_it	2.541
r_mcangle_it	1.915
r_mcbond_it	1.074
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.847
r_dihedral_angle_4_deg	18.92
r_dihedral_angle_3_deg	18.694
r_dihedral_angle_1_deg	7.273
r_scangle_it	3.793
r_angle_refined_deg	3.16
r_scbond_it	2.541
r_mcangle_it	1.915
r_mcbond_it	1.074
r_nbtor_refined	0.32
r_symmetry_hbond_refined	0.294
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.145
r_symmetry_vdw_refined	0.142
r_chiral_restr	0.1
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6668
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.