2VRP | pdb_00002vrp

Structure of rhodocytin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IOD	COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR
experimental model	PDB	1J34	COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR
experimental model	PDB	1C3A	COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR
experimental model	PDB	1UMR	COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		2M AMMONIUM SULPHATE, 5% 2-PROPANOL, pH 8

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.933	α = 90
b = 89.368	β = 90
c = 120.996	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	MIRRORS	2007-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.4	50	94.7	0.04	37.75	4		13367		-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	2.4	2.49	80.8		0.12	7.05	3.7

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	COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR	2.41	36.76	12040	618	94.4	0.204	0.201	0.2	0.272	0.28	RANDOM	38.94

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]
0.1			0.56		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.547
r_dihedral_angle_3_deg	22.436
r_dihedral_angle_4_deg	20.569
r_dihedral_angle_1_deg	8.822
r_scangle_it	3.438
r_scbond_it	2.161
r_angle_refined_deg	1.916
r_mcangle_it	1.704
r_mcbond_it	0.872
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.294
r_symmetry_hbond_refined	0.273
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.143
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2101
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing