Experiment: 2O84

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A8E	N-lobe human transferrin, PDB code 1A8E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	Protein: 35mg/ml, 0.1M ammonium bicrbonate. Well: 18% PEG3350, 0.2M potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.173	α = 90
b = 57.317	β = 90
c = 135.583	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MAR scanner 345 mm plate	osmic mirrors	2005-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

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	2.6	22.7	98.5	0.139	9	3.3	10917	10917			32.58

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)
	2.6	2.74	100		0.377	3	3.2	1576

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	N-lobe human transferrin, PDB code 1A8E	2.6	21.02	10358	10358	521	97.99	0.216	0.216	0.213	0.269	RANDOM	15.196

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]
0.02			0.07		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.633
r_dihedral_angle_4_deg	20.708
r_dihedral_angle_3_deg	16.26
r_dihedral_angle_1_deg	5.392
r_scangle_it	2.116
r_angle_refined_deg	1.273
r_scbond_it	1.257
r_mcangle_it	0.868
r_mcbond_it	0.46
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.633
r_dihedral_angle_4_deg	20.708
r_dihedral_angle_3_deg	16.26
r_dihedral_angle_1_deg	5.392
r_scangle_it	2.116
r_angle_refined_deg	1.273
r_scbond_it	1.257
r_mcangle_it	0.868
r_mcbond_it	0.46
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.205
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.087
r_metal_ion_refined	0.045
r_bond_refined_d	0.01
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2551
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
AMoRE	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.