2NLB | pdb_00002nlb

Human beta-defensin-1 (Mutant Asn4Ala)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	PEG 8000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.5, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.52	α = 90
b = 26.4	β = 100.8
c = 57.53	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	IMAGE PLATE	MAR scanner 345 mm plate	Osmic mirrors	2005-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54178

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	1.85	40	99.9	0.08	17.1	5.2	12053	12053		-3

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)
1	1.85	1.92	99.6		0.255	6	5	1178

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1IJV	1.85	30	12045	12045	577	99.77	0.182	0.182	0.179	0.19	0.238	RANDOM	21.632

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		0.84	-0.21		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.744
r_dihedral_angle_4_deg	27.592
r_dihedral_angle_3_deg	13.612
r_dihedral_angle_1_deg	5.506
r_scangle_it	3.169
r_scbond_it	2.23
r_angle_refined_deg	1.523
r_mcangle_it	1.483
r_mcbond_it	1.013
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.744
r_dihedral_angle_4_deg	27.592
r_dihedral_angle_3_deg	13.612
r_dihedral_angle_1_deg	5.506
r_scangle_it	3.169
r_scbond_it	2.23
r_angle_refined_deg	1.523
r_mcangle_it	1.483
r_mcbond_it	1.013
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.184
r_symmetry_vdw_refined	0.174
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1072
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	25

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	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.