5NTY | pdb_00005nty

Structure of non-fluorescent human plasma RBP4

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS		279	4.5M NaCl, 20mM Na cacodylate, pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.77	α = 90
b = 103.77	β = 90
c = 73.94	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2015-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0	ESRF	ID29

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	40	98.5	0.106	7.9	4.4		19780

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	2	2.11	98.3		0.491	2.5	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1brq	2	30	18786	990	98.52	0.17501	0.17198	0.21	0.23031	0.23	RANDOM	55.543

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]
-1.17	-0.59		-1.17		3.81

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	34.557
r_dihedral_angle_2_deg	32.524
r_sphericity_free	30.891
r_rigid_bond_restr	20.267
r_long_range_B_other	16.626
r_long_range_B_refined	16.558
r_scangle_other	15.869
r_dihedral_angle_3_deg	14.773
r_dihedral_angle_4_deg	14.75
r_scbond_it	14.555
r_scbond_other	14.546
r_mcangle_other	13.655
r_mcangle_it	13.651
r_mcbond_it	12.634
r_mcbond_other	12.625
r_dihedral_angle_1_deg	9.096
r_angle_other_deg	1.136
r_angle_refined_deg	0.605
r_chiral_restr	0.032
r_bond_other_d	0.005
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1408
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing