5PB5 | pdb_00005pb5

human factor VIIa in complex with 1-[[3-[5-hydroxy-4-(7H-pyrrolo[2,3-d]pyrimidin-6-yl)pyrazol-1-yl]phenyl]methyl]-3-phenylurea at 1.84A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		inhouse model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.037	α = 90
b = 95.037	β = 90
c = 116.512	γ = 90

Symmetry
Space Group	P 41 21 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	IMAGE PLATE	MAR scanner 345 mm plate		2008-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54177

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.84	49.67	98.5	0.063	0.063	22.22	9.57		46187

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)
1	1.84	1.94	90.1		0.363	0.363	4.5	7.07

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	inhouse model	1.84	47.51	43544	2320	98	0.186	0.1853	0.19	0.1998	0.21	RANDOM	23.166

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]
-0.38			-0.38		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.585
r_dihedral_angle_4_deg	16.859
r_dihedral_angle_3_deg	13.883
r_dihedral_angle_1_deg	6.466
r_scangle_it	2.85
r_angle_other_deg	2.055
r_scbond_it	1.662
r_angle_refined_deg	1.427
r_mcangle_it	1.303
r_mcbond_it	0.693

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.585
r_dihedral_angle_4_deg	16.859
r_dihedral_angle_3_deg	13.883
r_dihedral_angle_1_deg	6.466
r_scangle_it	2.85
r_angle_other_deg	2.055
r_scbond_it	1.662
r_angle_refined_deg	1.427
r_mcangle_it	1.303
r_mcbond_it	0.693
r_mcbond_other	0.119
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2346
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SADABS	data scaling
PHASER	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.