1L5T | pdb_00001l5t

Crystal Structure of a Domain-Opened Mutant (R121D) of the Human Lactoferrin N-lobe Refined From a Merohedrally-Twinned Crystal Form.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LCT	pdb entry 1lct

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	8	298	concentrated solution of the protein (50-80 mg mL-1), 0.01 M Tris-HCl, pH 8.0, 12% (v/v) isopropanol, MICRODIALYSIS, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.35	71.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.3	α = 90
b = 151.3	β = 90
c = 48.6	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	IMAGE PLATE	RIGAKU RAXIS IIC	graphite monochromator	1994-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	3	50	96	0.115	6.1	2.8		23431	4

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)
	3	3.11	93		0.418	0.418	1.8	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1lct	3	10	2	4	23431	21955	795	93.9	0.1413	0.139	0.13	0.199	0.18	RANDOM, PLUS TWIN-RELATED MATES	31.1

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		5241

RMS Deviations
Key	Refinement Restraint Deviation
s_from_restr_planes	0.177
s_non_zero_chiral_vol	0.03
s_similar_adp_cmpnt	0.026
s_zero_chiral_vol	0.023
s_angle_d	0.017
s_anti_bump_dis_restr	0.017
s_similar_dist	0.012
s_bond_d	0.005
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5114
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
ROTAVATA	data reduction
X-PLOR	model building
BRUTE	model building
SHELXL-97	refinement
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing
BRUTE	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.