2RL9 | pdb_00002rl9

Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to trimannoside

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	292	0.1M cacodylate, 25% PEG5000MME, 0.2M ammonium sulfate, pH 6.5, vapor diffusion, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.628	α = 90
b = 92.628	β = 90
c = 85.594	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	IMAGE PLATE	RIGAKU RAXIS IIC	osmic mirrors	1999-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	40		0.07		5.3		10608

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.4	30	10608	556	70.3	0.199	0.19	0.265	0.26	24.161

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]
-3.122			-3.122		6.244

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.888
c_mcangle_it	2.358
c_scbond_it	1.884
c_mcbond_it	1.379

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2355
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	106

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction

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.